If you have made custom changes to a WordPress theme and don’t want to upgrade to a new version, that is offered to you, open style.css in theme’s directory.
At the top you will find a big comment with theme’s version, name, author information etc.
Change the version in this comment to a big number, e.g. 9.9

Before:

Version: 1.7

After:

Version: 9.9

Go to WordPress update screen and update for this theme will disappear.