När hennes hals känns bättre, äter hon lite soppa, och då mår magen bättre.

Because Swedish has verb-second word order in main clauses.

The sentence starts with a subordinate clause: När hennes hals känns bättre = When her throat feels better.

After that whole clause, the main clause begins. In a Swedish main clause, the finite verb usually comes in second position, so you get:

• När hennes hals känns bättre, äter hon lite soppa.

Not:

• När hennes hals känns bättre, hon äter lite soppa. ✗

This is very common in Swedish:

• När jag kommer hem, äter jag.
• Om det regnar, stannar vi hemma.

So the inversion happens because the sentence does not begin with the subject of the main clause.

Because sin/sitt/sina refers back to the subject of the same clause.

In the clause:

• hennes hals känns bättre

the grammatical subject is hals (throat), not hon (she).

So sin cannot naturally refer to hon here, because hon is not the subject of that clause. That is why Swedish uses hennes.

Compare:

• Hon tvättar sin bil. = She washes her own car.
  Here hon is the subject of the clause, so sin works.

But in your sentence, the clause is built around halsen being the subject:

• Hennes hals känns bättre.

So hennes is correct.

Swedish often describes body parts directly as the thing that feels better:

• Halsen känns bättre. = The throat feels better.
• Benet känns bättre. = The leg feels better.

This is very natural Swedish.

The verb kännas means something like:

• feel
• seem
• feel like it is

So hennes hals känns bättre literally means her throat feels better, which is idiomatic in both Swedish and English.

They are related, but not identical.

• känns bättre is used for how something feels
• mår bättre is used for well-being, especially of a person, but also sometimes body parts in a more idiomatic way

In this sentence:

• hennes hals känns bättre = her throat feels better
• magen mår bättre = the stomach feels better / is doing better

Why the difference? Because Swedish often uses:

• kännas for a direct sensation
• må for general condition or wellness

For example:

• Jag mår bättre. = I feel better.
• Min mage mår bättre nu. = My stomach feels better now.

You could sometimes hear magen känns bättre too, but mår bättre sounds very natural when talking about the stomach or digestion.

Here då means something like:

• then
• at that point
• as a result

So:

• ..., och då mår magen bättre.

means:

• ..., and then her stomach feels better
• ..., and as a result her stomach feels better

It connects the second part to what came before: first she eats a little soup, and then / because of that the stomach feels better.

Swedish very often uses the definite form for body parts when it is already clear whose body part is meant.

So instead of saying:

• her stomach

Swedish often says:

• magen = the stomach

if the owner is obvious from context.

That is why:

• då mår magen bättre

sounds natural.

This is common with body parts:

• Jag tvättar händerna. = I wash my hands.
• Hon bröt benet. = She broke her leg.

English usually prefers a possessive like my / her / his, but Swedish often prefers the definite form.

Because lite here means a little or some, not small.

• lite soppa = a little soup / some soup

Soup is usually treated as an uncountable substance here, so Swedish uses lite directly before the noun.

By contrast:

• en liten soppa would mean a small soup, which sounds odd unless you mean something like a small serving or a small bowl in a very specific context.

So:

• lite soppa = quantity
• liten = size

Because soppa is being used as an uncountable noun here.

With quantity words like lite, Swedish usually does not add an article:

• lite vatten = a little water
• lite kaffe = a little coffee
• lite soppa = a little soup

This is similar to English, where we also say some soup or a little soup, not usually a soup in this meaning.

När means when.

It introduces a subordinate clause:

• När hennes hals känns bättre = When her throat feels better

This can refer to:

• a time in the future
• a repeated situation
• a general sequence of events in a story

So in this sentence, när sets up the condition in time: when her throat improves, she eats a little soup.

Because Swedish often uses the present tense for:

• general truths
• habitual actions
• narrative descriptions
• future situations when the context already makes the time clear

So this sentence can sound like:

• a general pattern
• a story being told in the present
• a situation that happens once the throat gets better

Swedish does this very naturally.

If you wanted to make the future more explicit, you could say something like:

• När hennes hals känns bättre ska hon äta lite soppa.

But the original present tense version is perfectly normal.

bättre is the comparative form of bra.

• bra = good / well
• bättre = better
• bäst = best

In the sentence:

• känns bättre
• mår bättre

it means feels better or is better.

This is a very common word, and you will often see it with verbs like:

• må bättre = feel better
• bli bättre = get better
• kännas bättre = feel better

The commas help separate the parts of the sentence:

• När hennes hals känns bättre,
• äter hon lite soppa,
• och då mår magen bättre.

The first comma, after the när-clause, is very natural because that introductory subordinate clause is fairly long.

The comma before och is more stylistic. In modern Swedish, commas before och are often omitted, especially in simple sentences, but writers may still use them to make the structure clearer.

So the punctuation here is understandable and natural, even though comma usage can vary a bit by style.