Salam Davood jan, It strictly depends on the reason why you are unable to catch the bus. Are you simply talking of the condition of not taking the bus? In this case, as others have mentioned "don't" would be more appropriate. Or are you talking with respect to a context in which you have indicated there is some obstacle (physical or not) getting in the way of you taking the bus (e.g. laziness, logistics, a barrier, a large crowd making it impossible to board the bus, etc.)? In that case "can't" would be the appropriate way of expressing your intended meaning.

Hi, Davood! Yes, this sentence is correct and natural. However, some English speakers will prefer that you say "If I DON'T catch the bus, I'm going to be late," because "can" in the strictest sense means "to have the ability to." Obviously, you have the ability to catch the bus, but perhaps on this day, there is an obstacle blocking you from doing so; therefore, "don't" might be more fitting. I hope this helps. Please let me know if my answer is confusing.

This sounds better: "If I don't catch the bus, I'm going to be late."

It's not correct for two reasons. 1: This is an IF clause (conditional) and therefore you must use will. If I can't catch the bus, I'll be late. 2: Will is used for predictions and other future actions/events that we decide in the moment we are speaking. Meanwhile "going to" is used for intentions for the future or things that you have already decided on in the past. You don't intend to be late, and the thing that decides if you will be late has not happened yet.