Hello there, Anoop.
You can either un-check the Tax box or choose Out-of-Scope from the Tax drop-down menu on the invoice. This is to ensure that both transactions matched.
Here's a sample screenshot of what it looks like:
I'm also adding this article that contains information on how to enter and apply a credit memo.
You can always leave a reply if you have additional questions about invoices in QuickBooks. Thanks.