Ich nicke nur, obwohl ich innerlich seufze.

Because the sentence is in the present tense, and both verbs are conjugated for ich.

• ich nicke = I nod
• ich seufze = I sigh

For regular verbs in German, the 1st person singular usually ends in -e in the present tense.

• nicken → ich nicke
• seufzen → ich seufze

So the -e here is just the normal ending for ich.

Here, nur means something like just, simply, or only.

So Ich nicke nur suggests:

• I do nothing more than nod
• I merely nod
• I just nod

It often gives the sentence a slightly restrained feeling, as if the speaker is keeping their reaction minimal.

Because obwohl introduces a subordinate clause, and in German, subordinate clauses are normally separated from the main clause by a comma.

So:

• Ich nicke nur, obwohl ich innerlich seufze.

This is standard punctuation in German. You will also see commas before other subordinating conjunctions like:

• weil
• dass
• wenn
• obwohl

Because obwohl is a subordinating conjunction, and subordinating conjunctions send the conjugated verb to the end of the clause.

Main clause:

• Ich nicke nur

Subordinate clause:

• obwohl ich innerlich seufze

That final verb position is one of the most important word-order rules in German subordinate clauses.

Compare:

• Ich seufze innerlich.
  normal main clause word order

• ..., obwohl ich innerlich seufze.
  subordinate clause, so the verb moves to the end

Obwohl means although / even though. It introduces a contrast, but specifically a concession: something happens despite something else.

So the idea is:

• I nod, although inwardly I am sighing.

That is slightly different from aber (but).

• aber connects two main clauses
• obwohl introduces a subordinate clause

Compare:

• Ich nicke nur, aber ich seufze innerlich.
• Ich nicke nur, obwohl ich innerlich seufze.

Both show contrast, but obwohl feels more like despite the fact that.

Because the second part is a full clause of its own, and German normally needs an explicit subject there.

So you get:

• ..., obwohl ich innerlich seufze

Even though the subject is the same person, German does not drop ich here.

Each finite clause generally needs its own subject, especially when the second one is a subordinate clause introduced by obwohl.

Innerlich means inwardly, internally, or inside.

It tells you that the sigh is not necessarily audible or outwardly visible. The person may look calm on the outside, but internally they are reacting with frustration, weariness, or resignation.

So innerlich seufzen is a very natural way to express:

• to sigh inwardly
• to sigh to oneself
• to feel an internal sigh

Because nicken can be used intransitively, just like to nod in English.

So:

• Ich nicke. = I nod.

No object is required.

If needed, German can add more information, for example:

• jemandem zunicken = to nod to someone
• mit dem Kopf nicken = to nod with one’s head

But in your sentence, the simple intransitive use is enough.

It is in the present tense:

• ich nicke
• ich seufze

In German, the present tense often covers both:

• simple present: I nod
• present progressive: I am nodding

So depending on context, the sentence could sound like either a general present description or something happening right now.

In colloquial spoken German, yes, you may sometimes hear obwohl followed by main-clause word order. But in standard written German, the normal and correct pattern is the one in your sentence: verb at the end.

Standard:

• ..., obwohl ich innerlich seufze.

Colloquial spoken German sometimes:

• Obwohl, ich seufze innerlich.

That spoken pattern is common in conversation, but learners should first master the standard structure with the final verb.

Because innerlich is an adverb, and in this subordinate clause it naturally appears before the final verb.

So the clause is:

• obwohl ich innerlich seufze

This is a very normal position in German. Since the verb goes to the end in a subordinate clause, other elements like adverbs often appear before it.

You could think of the structure as:

• obwohl
  • subject + adverb + verb

So:

• obwohl
  • ich
    • innerlich
      • seufze