1. He cannot have cleaned his room.
2. It is impossible that he cleaned his room.
3. He could not have cleaned his room.
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#1 mean #2, right? Then What is the meaning of #3? Would you write another sentences having similar meaning?
All three mean the same thing.
I can't believe he cleaned his room already.
I'd be surprised if he cleaned his room by now.
Yes, sentence #1 and sentence #2 convey the same meaning - the assertion that it is impossible for him to have cleaned his room.
Sentence #3, "He could not have cleaned his room," also expresses the same meaning as sentences #1 and #2. It suggests that there is very little or no possibility that he cleaned his room.
Here's another sentence with a similar meaning: "It is highly unlikely that he cleaned his room." This sentence conveys the idea that the probability of him cleaning his room is extremely low.