Which sentence is correct?
Does it change anything?
Is it changes anything?
How would native speaker say something like this?
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You are correct that the first example is grammatical and the second is not.
English speakers use auxilliary (or helping) verbs in front of nouns and pronouns to ask questions, with the main verb following. For example, they say:
Does it change (something)
Will it change (something)
Might it change (something)
In each case it itself might change or you could add something (an object, using the verb transitively.)
And in the past:
Has it changed (something)
Had it changed (something)
Did it change (something)
Adding an object makes the difference between saying:
He has changed since I saw him last (intransitive)
He has changed his clothes since I saw him last. (transitive)
However, you cannot add an object after is and was.
So you can legitimately ask:
Is it changed
meaning has it undergone a change itself
but you cannot say:
Is/was it changed something
You have to ask:
Has it changed something
Did it change something