First of all, make sure you have Mono installed. MonoDevelop does not include Mono runtime, so you will have to install it separately.
Once you set the Mono runtime, there are several ways to select the .NET toolchain that will be used to create and run applications.
If you plan to build and run mainly on Mono, you can set Mono runtime as the standard runtime for MonoDevelop. To do this, go to Edit-> Preferences → .NET Runtimes, select Mono runtime, and click "Choose Default."
Mono , Project- > Active Runtime .