This simply means that the outcome is changed or will be changed by "it". This usually indicates a positive change, rather than a negative one, but that can also depend on the specific change that is made. When using "a", the effect on the outcome is usually small or ambiguous. When using "the", the change is usually something known or the outcome is decided by the change.
For example, you might say "He gave $10 to a homeless man. There are thousands of homeless people, but it makes a difference to that man." This is a small change. The man is still homeless, but perhaps he can buy some food.
"I want to buy a house, but I need a bank loan. It makes the difference." This means that if the speaker does not get a loan from a bank, he will not buy a house. The outcome is decided by the change of having a loan.