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.
Under "Merge button", select Allow rebase merging. This allows contributors to merge a pull request by rebasing their individual commits onto the base branch.
If you also select another merge method, collaborators will be able to choose the type of merge commit when merging 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."