Even you have access to your server as root using WHM web interface access, root access using SSH doesn't need to be enabled by default.
To enable root access through SSH client (e.g. putty, terminal or ssh command line tool) follow these steps:
1. Login to your WHM panel
2. go to Security -> Manage Wheel Group Users and make sure your user is in the Wheel group (this group defines who is able to use su command)
3. Now you should be able to login with user assigned to wheel group using ssh and once you are in, you can login as root using command: