Does Fortitoken MFA support the server that running on Windows server 2012?

You mean when logging in with FortiAuthenticator agent?

Yes, FortiToken MFA fully supports Windows Server 2012 and 2012 R2. To implement this, you need to deploy the FortiAuthenticator Agent for Microsoft Windows on your target server.

The agent acts as a Windows Credential Provider plugin. It intercepts the login sequence, prompts the user for their FortiToken OTP, and validates it against the FortiAuthenticator via REST API before processing the standard Active Directory password.