In a literal sense, "make one's bed" refers to straightening the sheets, blankets, and pillows. Normally, one would do that when one gets out of it, so it is tidy. It doesn't really make sense to make one's bed before you get into it.
There is also a figurative sense of "makes one's bed" that refers to one being responsible for the circumstances one has created.
Let's say John cheats on his wife and gets caught. When the wife files for divorce, one could say, "John made his bed and now he has to lie in it."