About auto-closing issues
By default, merging a linked pull request automatically closes the associated issue. You can override the default behavior by disabling auto-closing.
Enabling or disabling auto-closing of issues
- 
On GitHub, navigate to the main page of the repository. 
- 
Under your repository name, click Settings. If you cannot see the "Settings" tab, select the dropdown menu, then click Settings.  
- 
Under General, scroll down to the Issues section. 
- 
Select or deselect Auto-close issues with merged linked pull requests to enable or disable auto-closing.