1) What do you think is the reason (that ...) or ( for...) <something>. Usually some clause follows this construct. The original is correct, but you wouldn't see it as often as (2) 2) Is correct 3) What is the reason, do you think? [Notice the comma]

Hi there, Let's see... All three of these sentences would be quite easily understood by native speakers. However, I think sentence 2 is the strongest. It the most direct. 1.)What do you think the reason is. This looks like 2 questions; What do you think? + What is the reason? 2.)What do you think the reason is? - This is very specific and to the point. 3.)What is the reason do you think? This one is the weakest. Again it is made up of two questions. What is the reason? + What do you think? - This time the word order has been changed. Does this make sense? In casual speaking any of these would be fine. When we are talking amongst friends our thoughts tend to be disorganized. Therefore, we often string together sentences like these when we are not careful, but they are still understood. Cheers!

By the way, the proper way to ask this question is "Are all of these sentences grammatically correct?"

The second is correct because "do you think" is the inverted verb-subject that makes the sentence a question. "The reason is" is the object of the sentence; there is no reason to invert the subject and verb. Americans frequently say the first and, similarly, use noun clauses incorrectly. For example, people sometimes say, "I wonder what is she going to do today?" But a noun clause ("what she is going to do today) is acting as a noun (subject or object) and, therefore, the subject-verb order should not be inverted. The correct way to say this is "I wonder what she is going to do today."

thank you! and thank everyone who answers me!