1. If you're asking a direct question, the correct form is this:
"What is his destination?"
This is the interrogative form, where the verb ( 'is') has to come before the subject ('his destination').
2. If these four words are part of a longer sentence, either an embedded or indirect question, you use the affirmative form. In the affirmative form, we put the subject before the verb. For example:
I'll ask him what his destination is.
We need to know what his destination is.
Can you tell me what his destination is?
I hope that helps.