"What do you say it" doesn't make sense. If you want to know how to pronounce a word or to know which is the right word to what you're thinking, then the correct form is "how do you say____?" whatever you want to put on the blank space.

You have two choices: How do you say it? What do you say? In the first sentence, you want to know the method. (How do you say ______?) For example, "How do you say 'computer' in French?" or "How do you pronounce 'can' in English?" In the second sentence, you want to know the thing that you say. For example, "What do you say when you bump into someone by accident?" You say, "Excuse me." We also use "What do you say?" when we want someone's opinion. "Let's eat sushi. What do you say?"

The what one is simply wrong, you could say "what do you call it", though.