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Fred and George looked at each other. Then Fred said abruptly, “I've told you before, Ron, keep your nose out if you like it the shape it is. Can't see why you would, but -”

I don't know how to understand the grammar of "you like it the shape it is". It seems to me that "you like it with the shape it is" looks more grammatical. How should we understand the grammar of the sentence?

• Excerpted from Harry Potter.

It is syntactically analogous to the way it is.

I like it the way it is.

That is, "as it is (now)".

If you like the present shape of your nose, butt out.

Would you like some more milk to cool your tea down?

-- No thanks, I like it the temperature it is.

or

Shall we keep the room the color it is?

The conveyor belt is working out nicely. Let's keep it the speed it is.

P.S. This pattern works with intrinsic attributes (shape, color, speed, temperature, age, height, width, etc). the [attribute] it is doesn't work with the extrinsic:

Shall I add more cumin?

-- No, I like it the taste it is. ^marginal

or

Should we make our games for children ages 7-10 more difficult? Are they challenging enough?

-- Let's keep them the difficulty they are. ^marginal

or

Shall we add a torx bit to our multi-function tool? Is the tool's usefulness competitive?

-- No, let's keep it the usefulness it is. ^{ungrammatical}

or

There have been many fatalities in our new Corvair model. Shall we do something about the car's safety?

-- No, let's keep it the safety it is. ^{ungrammatical}

"I've told you before, Ron, keep your nose out if you like it the shape it is. Can't see why you would, but—"

From the context, this is colloquial speech, not formal speech. Artistic license and regional dialects or character-driven speech patterns may differ from strict grammar rules in this type of writing.

Even so, this example seems like a fine (if informal) literary construction to me. It is roughly equivalent to:

Keep your nose out [of my business / things that don't concern you] if you like...[your nose] the shape it is [currently in].

Here, "it" is used twice as a pronoun that refers to Ron's nose. Given the context, and the somewhat clipped speech pattern of the character being quoted, various words have been elided by the author in a way that still seems clear to me while invoking various common idioms about "being nosey" and related risks.

In this case, the apparent meaning is that Ron is intruding into something Fred thinks is none of Ron's business (e.g. sticking his nose in). Fred is either making a physical threat (i.e. Ron may get punched in the nose) or using a somewhat witty metaphor to imply that such behavior is risky for Ron.

In the second sentence:

"Can't see why you would, but—"

is probably a not-so-subtle put-down. Without additional context it's hard to be sure, but it reads as if Fred is calling Ron's nose ugly. Another way to think about this colloquial sentence pair might be to restructure it to see how the insult follows the threat:

Mind your own business if you like the current shape of your nose. I don't know why you would like it since it's so ugly, but it's probably still good advice to keep your nose out of other people's business if you don't want to get it broken.

Taken together, this is most likely the semantic meaning of the two sentences you posted. However, it loses a lot of the flavor of the original prose. Presumably, the original construction is more consistent with the rest of the material, and certainly seems more colorful.