This is a phrase to say when something disappointing happens. It means that you're disappointed, but you're not going to get too upset about it.
Here's another example:
It's not the end of the world if we fall a few thousand dollars short of our sales target, but we certainly don't want to end up short by more than 10 percent.
You can think of "It's not the end of the world" as an example of understatement. You're saying that the disappointing thing is not as bad as the world ending. But of course it's not, because the world ending is probably the worst thing that could ever happen!
So "It's not the end of the world" is an understated way to say that the situation is bad, but not too bad.