Learn Hardcore Chinese: zài dàxué lǐ, tā tèbié xǐhuan lìshǐ kè hé dìlǐ kè. - At university, he especially likes history class and geography class.

The version in your sentence puts 在大学里 at the very start, which slightly emphasizes the setting at university / during his college years. The version with 他在大学里… is a bit more neutral, emphasizing he first. Grammatically, both word orders are correct; the difference is mainly nuance and emphasis, not meaning.

What is the difference between 在大学里, 在大学, and just 大学?

在大学里 – literally inside / at the university. Very natural and common when talking about things that happen while you are in college.
在大学 – also at the university / in college. For this kind of place word, adding 里 is optional; 在大学 and 在大学里 usually mean the same thing in everyday speech.
Bare 大学 by itself here would not work as a full modifier of the verb. You need something like 在大学里, 上大学的时候, or 读大学的时候 to express when/where the action happened.

So 在大学 vs 在大学里: almost no difference here. Leaving out 在 and saying only 大学，他特别喜欢… is not grammatical.

Why do we use 里 after 大学? Is 里 always needed after place words?

里 (lǐ) means inside / within and is often added after nouns that are thought of as enclosed spaces:

在教室里 – in the classroom
在家里 – at home
在学校里 – at school

With many such place words, you can use either 在大学 or 在大学里, and they feel almost the same. 里 can make it sound a bit more like within that environment, but here the difference is tiny.

It is not always used:

We say 在北京, not 在北京里.
We say 在中国, not 在中国里.

So you add 里 mostly for places that are naturally seen as an interior or a bounded space; for large regions or countries you normally do not.

In English we say liked (past tense), but in Chinese it is just 喜欢. Why is there no past tense marker like was / did / -ed?

Chinese verbs do not change form for tense (no -ed, no -s, etc.). Time is shown through:

Context
Time expressions
Aspect particles like 了, 过, 着 (when needed)

In this sentence, 在大学里 already tells you we are talking about a past period of his life (when he was in college), so Chinese does not need to change 喜欢 or add anything.

If you want to make the past time even clearer, you can say:

在大学里的时候，他特别喜欢历史课和地理课。
(When he was in college, he especially liked history and geography classes.)

You would not say 特别喜欢了 here; that sounds wrong in this context. The simple 特别喜欢 plus the time phrase is the natural way.

What exactly does 特别 add to the meaning? How is 特别喜欢 different from 很喜欢?

Both 很 and 特别 can intensify 喜欢, but they feel a bit different:

很喜欢 – really / very much likes. It just shows a high degree.
特别喜欢 – especially / particularly likes, often implying:
- Either he likes it more than average, or
- He likes it more than other subjects.

So:

他很喜欢历史课。 – He really likes history class.
他特别喜欢历史课。 – Among all his classes, history is a standout favorite.

In your sentence, 特别喜欢 suggests those courses were special favorites, not just generally liked a lot.

Why is 特别 placed before 喜欢? Could I say something like 他喜欢特别历史课?

In Chinese, adverbs almost always come before the verb or adjective they modify. So:

特别喜欢 – correct (adverb before the verb)
经常去 – often go
非常大 – very big

So 他特别喜欢历史课 is the normal structure.

If you say 他喜欢特别历史课, it sounds like you are saying he likes special history classes (with 特别 modifying 历史课 as an adjective). To do that properly you would usually say:

他喜欢特别的历史课。 – He likes special history classes.

In your sentence we want especially likes, not special history, so 特别 must go before 喜欢: 特别喜欢.

Why do we need 课 after 历史 and 地理? Can we just say 他特别喜欢历史和地理?

You can say 他特别喜欢历史和地理; that is also grammatical and natural.

The difference is:

历史 / 地理 by themselves refer to the subjects / fields of history and geography.
历史课 / 地理课 refer more specifically to the courses / classes in those subjects.

In the context of 大学, talking about history class and geography class feels very natural, because you take them as courses. If you drop 课, the sentence shifts slightly toward he especially liked the subjects of history and geography (still fine). Including 课 just makes it explicit that we are talking about classes.

Why is 课 repeated after both 历史 and 地理? Could I say 历史和地理课 instead?

All of these are possible, but they have slightly different feels:

历史课和地理课
- Repeats 课, clearly marking both as separate courses.
- Very clear and common in speech and writing.
历史和地理课
- Grammatically okay, and usually understood to mean history and geography class(es).
- However, in theory it could be read as history (as a general field) and geography class (more specific). Context usually prevents confusion, but this structure is a bit less balanced.
历史课和地理
- Asymmetrical: history class and geography (as a subject). This sounds a bit odd unless you have a special reason.

Repeating 课 in 历史课和地理课 makes the list nice and parallel and avoids any ambiguity. That is why many speakers naturally repeat it here.

How does 和 work here? Is it the same as English and? How is it different from 也 or 跟?

In this sentence, 和 (hé) is a coordinating conjunction that simply links two nouns:

历史课和地理课 – history class and geography class

Comparison:

和 vs 也:
- 和 links nouns / noun phrases:
  - 历史课和地理课 – history class and geography class
- 也 is an adverb meaning also / too, and it goes before the verb:
  - 他喜欢历史课，也喜欢地理课。 – He likes history class; he also likes geography class.
- So you cannot replace 和 here with 也.
和 vs 跟:
- When linking nouns, 和 and 跟 are often interchangeable in everyday speech:
  - 历史课跟地理课 – history class and geography class
- 跟 is also common as a preposition meaning with:
  - 跟朋友一起上课 – attend class with friends
- 和 can sometimes do that too, but 跟 is more colloquial in the with-meaning.

So in your sentence, 和 is functioning just like English and, linking two course names.

Could we say 他在大学里特别喜欢历史课和地理课 instead? Is that different from 在大学里，他特别喜欢…?

Yes, 他在大学里特别喜欢历史课和地理课。 is completely correct.

Both versions:

在大学里，他特别喜欢历史课和地理课。
他在大学里特别喜欢历史课和地理课。

mean the same thing. The difference is very slight:

Sentence-initial 在大学里 puts a bit more emphasis on the setting / period (during his college years).
他在大学里… is slightly more neutral and starts from the person.

Native speakers freely use both; in many contexts they are interchangeable.

If I want to say he especially liked one history class, how do I add a measure word for 课?

For courses / subjects like 历史课, the common measure word is 门 (mén).

Examples:

一门历史课 – one history course
两门地理课 – two geography courses

So you could say:

在大学里，他特别喜欢一门历史课。
– In college, he especially liked one (particular) history course.

If you want to keep both subjects and count both:

在大学里，他特别喜欢一门历史课和一门地理课。

Note that adding 一门 makes it sound like you are referring to specific individual courses. If you are talking about the subjects in general, you normally do not add the measure word here and just say 历史课和地理课.

Can I replace 喜欢 with 爱 in this sentence? Would 他特别爱历史课和地理课 sound natural?

You can say 他特别爱历史课和地理课, but it feels stronger and more emotional.

喜欢 – to like, from mild to quite strong, but still sounds neutral and safe in most contexts.
爱 – to love, usually:
- Stronger feelings: romantic love, family love.
- Or a very strong preference: 我爱音乐, 我爱足球.

For school subjects and classes:

特别喜欢历史课和地理课 – sounds like: those were his favorite classes; very natural.
特别爱历史课和地理课 – sounds like he has a real passion for them; it is not wrong, but it is a bit more dramatic or literary.

For everyday description of preferences, 喜欢 is generally the safer, more typical verb.

How do we know whether 他 means he or she here? Is the pronunciation different?

In modern Mandarin:

他 (he), 她 (she), and 它 (it) are all pronounced the same: tā (first tone).

So in 他特别喜欢历史课和地理课, if you only hear the sentence, you cannot tell from the sound whether it is he or she; you rely on context.

In writing, different characters show the gender:

他 – usually he, but also historically used as a generic he / she.
她 – specifically she.
它 – it (things, animals, abstract entities).

Your sentence uses 他, so on the page it clearly means he. In speech, tā could refer to a man or a woman; only the surrounding conversation will make it clear.