Both questions are fine. Your second one should have 'one' rather than 'it', apart from that, both questions, and both answers are fine, and interchangeable. The 'do you have' form is possibly more common in US English, but both would be understood anywhere.

The natural answers are as follows: "Do you have a car?" -- "No, I don't" (or "Yes, I do"). "Have you got a car?" -- "No, I haven't" (or "Yes, I have").

1. First, your question about 'Do you have a car?' and 'Have you got a car?'. Yes, they are identical in meaning and can be used interchangeably. The 'got' construction is slightly more informal, but it is fine to use it in casual and neutral spoken English. It is used less in formal situations. 2. Secondly, the answers. As James says, it is normal to 'echo' the question when we give short answers. We do this by repeating the first verb in the question 'Have you got a car?' Yes, I have. 'Have you got a car?' No, I haven't. 'Do you have a car?' Yes, I do. 'Do you have a car?' No, I don't. Native speakers do this 'echo' thing without thinking. It's like a game of ping-pong. 3. Thirdly, he pronoun 'it' is a definite pronoun, referring to a specific known or previously mentioned subject. The equivalent indefinite pronoun is 'one'. Have you got a car? No, I haven't got one. This is a question about cars in general - 'a car' can be any car at all. Have you got the car? No, I haven't got it. This refers to a specific car. For example, if a husband and wife meet in town after work, one might ask the other if they have brought the family car. In this case 'the car' means a specific car, and both people know which car they are referring to. 4. Finally, it's important to remember that you can only use the 'Have you got..?' form in the present tense, and when it refers to possession of some kind - basically the equivalent of 'tener' in Spanish. In all other tenses and in all other situations, you have to use the 'Do you have..?' form. You can't use 'have got' when 'have' represents an action or another verb ( for example 'Do you have breakfast late on Saturdays?), and you can't use it when 'have' is an auxiliary verb ('haber' in Spanish).