This idiom or expression like sentence means:

The answer is “X”.
“X” is the important thing.
It’s the “X” that makes a difference. Etc.

If you say “It’s the winning that counts,” you mean something like:
The answer is the “winning”.
“Winning” is the important thing.
It’s the “winning” that makes a difference. Etc.

Examples:
It’s the spirit that counts.
It’s the money that counts.
It’s the end result that counts. Etc.