Why is the check charging system light staying on when you replaced the battery and alternator on a 2000 ford windstar?

You should just have to reset the system. You might also want to make sure that the battery and alternator are both working properly. The alternator especially could be defective. Most are rebuilt and sometimes not done that well. Just have someone with a tester check the system. If all this is fine it it an electrical problem, it could even be due to one of the recalls. Make sure that all the recalls are fixed. It cost nothing but time. Just go to Ford'd website and put your vin to check to see if you have any open recalls. There are at least two that I know you van has.