The Asian powerhouses, who have already booked their passage to the 2014 FIFA World Cup, outclassed the home side at a steamy Rajamangala Stadium with goals from Ashkan Dejagah, Reza Ghoochannejhad and Alireza Jahanbakhsh.
And the victory took unbeaten Iran to 10 points two games remaining in Group B, with Thailand still without a point and facing almost certain elimination.
"We go to Lebanon next week with 10 points which was our goal. I think it will be enough to qualify for the Asian Cup finals," said Iran coach Carlos Queiroz.
"It was a good game for us tonight, especially in the first half. We were 2-0 up and had control of the game after 45 minutes. We slowed down a bit in the second half and played with less energy and speed. My players know there is a long trip to Lebanon."