What will happened if we change AWS S3 access key and EC2 windows desktop password?

TL;DR: It depends on where you are using the credentials (access key and password) - it's not possible from this forum to directly determine what the impact will be. Therefore this advice is general only.

Changing the Windows password will affect anything that uses that password. If it's the password that you use to access the instance then you'll need to use the new password. If there are processes running on the instance that have the password hard-coded into them (this isn't a good security practice but it happens all the time) then those will need to be updated. If there are other resources in your VPC that are accessed by that user then those may be interrupted because the password has changed.

When you say "S3 access key" I assume you mean access and secret access key. If you change this, then anything that relies on that access key will need to be updated. For example, if the access and secret access key have been put into a credentials file for an application or for the AWS CLI to use then you'll need to update those files.

I'd add that EC2 instances can have roles attached to them and doing so means that you don't have to create static, long-lived credentials (access key and secret access key) in order to access AWS resources. Again, it's not possible to know what you're using the credentials for (that detail is not in your question) but if you are using long-lived credentials on an EC2 instance, I'd strongly recommend using roles instead.