In Ubuntu and other Linux distribution the “root” user is not directly accessible with a login operation without first doing an intermediate login with an unprivileged user.
Luckily, you can configure WinSCP to log in automatically from an unprivileged user into the “root ” user, by following these simply steps:
At the login window select:
1. File protocol: SCP
2. Advanced... (Advanced Site Settings)
3. Environment: SCP/Shell
4. Shell: sudo su -
5. select OK
Good luck!