Wenn dein Knie noch weh tut, sollst du es schonen.

Wenn introduces a condition and means if here.

So Wenn dein Knie noch weh tut, ... means If your knee still hurts, ...

A common point of confusion is that wenn can also mean when in other contexts. In this sentence, the meaning is conditional, so if is the natural English translation.

Also compare:

• Wenn es regnet, bleibe ich zu Hause. = If it rains, I stay home.
• Immer wenn es regnet, bleibe ich zu Hause. = Whenever it rains, I stay home.

Because dein Knie is the subject of the clause, so it is in the nominative case.

The verb phrase is weh tun = to hurt. In German, the thing that hurts is the grammatical subject:

• Mein Arm tut weh.
• Dein Knie tut weh.

So Knie is nominative, and the possessive has to match that:

• dein Knie = nominative neuter singular

You would use deinem Knie only in a dative context, for example:

• Ich schade deinem Knie nicht.

The expression is wehtun / weh tun, meaning to hurt.

In normal finite sentences, it is very often split:

• Mein Knie tut weh.
• Tut dein Knie weh?

In your sentence, the clause is introduced by wenn, so the conjugated verb goes to the end of the subordinate clause. That gives:

• Wenn dein Knie noch weh tut, ...

So tut is the finite verb, and weh stays together with it as part of the expression.

Here noch means still.

So:

• dein Knie tut weh = your knee hurts
• dein Knie tut noch weh = your knee still hurts

It shows that the pain has not gone away yet.

Because the sentence begins with a subordinate clause:

• Wenn dein Knie noch weh tut, ...

In German, when a subordinate clause comes first, the main clause follows with the verb in second position. The entire wenn clause counts as position 1, so the conjugated verb comes next:

• Wenn dein Knie noch weh tut, sollst du es schonen.

This is a very important German word-order pattern.

Compare:

• Du sollst es schonen, wenn dein Knie noch weh tut.
• Wenn dein Knie noch weh tut, sollst du es schonen.

Both are correct, but the second one causes inversion: sollst du.

Es refers back to dein Knie.

The noun das Knie is neuter, and its accusative singular form is also es when replaced by a pronoun.

So:

• das Knie → es

That is why German says:

• Du sollst es schonen.

In English we might also say it for a body part in this structure, although English often prefers repeating the noun or using a different phrasing.

Schonen means something like to go easy on, to spare, or to rest/protect from strain.

In this sentence, es schonen means:

• don’t put too much weight on it
• don’t strain it
• let it rest

This verb is especially common with body parts and injuries:

• den Rücken schonen = to go easy on your back
• das Bein schonen = to rest the leg / not strain the leg

So Du sollst es schonen is more natural than translating word-for-word as something like you should spare it.

Sollst usually expresses advice, instruction, or what someone is supposed to do.

So Du sollst es schonen is like:

• You should rest it
• You’re supposed to go easy on it

If you said musst, that would sound stronger:

• Du musst es schonen. = You must rest it.

So sollst is often softer or more like a recommendation, especially in health-related advice.

Yes, absolutely.

Both are correct:

• Du sollst es schonen.
• Du sollst dein Knie schonen.

Using es avoids repeating dein Knie, so it sounds more natural in many contexts. German often uses a pronoun once the noun has already been mentioned.

Yes. The word is:

• das Knie

So its pronoun is:

• es in nominative/accusative singular

This is why the sentence says es schonen.

It can be helpful to learn body-part nouns with their articles:

• der Arm
• das Bein
• das Knie
• der Rücken
• der Fuß

Yes. A very natural alternative is:

• Du sollst es schonen, wenn dein Knie noch weh tut.

The meaning stays the same. The difference is mostly about emphasis and style.

If the wenn clause comes first, it sets up the condition first:

• Wenn dein Knie noch weh tut, sollst du es schonen.

If the main clause comes first, the advice comes first:

• Du sollst es schonen, wenn dein Knie noch weh tut.

Mostly, yes, especially in beginner German.

Typical examples are:

• Mein Kopf tut weh.
• Der Rücken tut weh.
• Das Knie tut weh.

German can also use it emotionally in some contexts:

• Das tut weh. = That hurts.

But in a sentence like this one, it clearly refers to physical pain.

In German, subordinate clauses are separated by commas.

Since the sentence starts with the subordinate clause, the comma marks the end of that clause:

• Wenn dein Knie noch weh tut, sollst du es schonen.

If the subordinate clause came second, the comma would come before wenn:

• Du sollst es schonen, wenn dein Knie noch weh tut.

So the comma is required in both versions.