Humans have approximately 25000 genes. Why are these genes on 46 chromosomes? Why not 40 or 50?
According to this article, no one knows; it's an "evolutionary mystery." As a general rule, closely related species generally have a similar number of chromosomes, and the number typically increases with the complexity of the species. However, the actual number varies wildly.
The author also points, out,
Each egg or sperm gets 23 chromosomes (half of each pair). Which chromosome they get in the pair is totally random. When you do the math, this comes out to 10 trillion different possible combinations. If we had only one pair of chromosomes, the number drops to 4.