After admission, should I thank a recommender who I suspect wrote a bad letter? I have strong suspicion that one of the professors regardless of the professional relationship we had was not very nice in the recommendation letter. This is after knowing him at a personal level and how perfectionist and judgmental he is of other people. But let's not get into why I chose him to write my recommendation letter, you can assume I had my reasons. I got into the master's program I wanted which is one of the top in the US. 

But that was the only program I got into while other programs ranked much lower declined me. My grades were good and my record was good the two other recommendation letters were good for a fact, so that only leaves me to assume that this top college did not weigh in so heavily on his recommendation letter to make their decision. 

But all this is speculative, my question and concern is, should I let him know that I got into the program I wanted regardless? I want to do this as a courtesy and a thank you message. My fear is that he might go as far as approach the committee and ask for my admission to be re-evaluated. Or bad-mouth me to colleagues in that university if he knows I am attending.
Yes, you should thank and inform your letter writer, and no, you shouldn't worry about some bizarre and unrealistic "re-evaluation" of your admission.

Comments: It is very unlikely that your writer wrote a negative letter. In general, one only agrees to write a letter if one has something constructive or positive to say. Having read lots of letters, I'll note that even judgmental and perfectionist people put their criticisms in context, comparing to their general assessments of other students or researchers. (I.e. this person isn't perfect, but he/she is better than most others for the following reasons). These letters, in fact, are often the most compelling. 

As a further comment, you're being very uncharitable in assuming bad intentions of someone who agreed to write a letter for you! 

And a final comment: no university is going to care to "re-evaluate" their admission of you, even in the stunningly unlikely event that someone asks them to, except in cases of actual fraud, criminal issues, etc. Everyone involved has better things to be doing with their time.