You can configure pull request merge options on your GitHub Enterprise Server instance to meet your workflow needs and preferences for managing Git history. For more information, see "Configuring pull request merges."
On your GitHub Enterprise Server instance, 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 "Merge button", select Allow merge commits. This allows contributors to merge a pull request with a full history of commits.
If you select more than one merge method, collaborators can choose which type of merge commit to use when they merge a pull request. If there is a protected branch rule in your repository that requires a linear commit history, you must allow squash merging, rebase merging, or both. For more information, see "About protected branches."