Root user login in gnome is disabled on Debian system by default for security reasons. If you want to enable it for specific reasons then follow the below steps :
1. Login into Debian system
2. launch the Root Terminal from Applications -> Accessories.
3. Authenticate with password to launch the Root Terminal.
4. Open "/etc/pam.d/gdm3" with vi.
5. Look for "auth required pam_succeed_if.so user != root quiet_success" , comment it out as below.
#auth required pam_succeed_if.so user != root quiet_success
6. Save the modification with Esc+w+q+Enter keystroke.
7. Restart or reboot Debian system.
8. Login with root user in gnome. You should be now able to login successfully.