Your sentence: "that is in which restaurant we met yesterday?"
No, the sentence structure is incorrect. It seems to me that you are trying to transform your original sentence (That is the restaurant in which we met yesterday.) into a question. We often start a question in English using auxiliary verbs such as "Is". We also use "where" as a relative pronoun to provide more information about a location.
"Is (auxiliary verb to start a question) that (imagine that you are pointing to the restaurant) the restaurant (preceding noun) where we met yesterday?"
Just as a side discussion, you can also write your original sentence as: "That is the restaurant [where] we met yesterday."
I hope this helps you.