Can we configure different MTU for sub interfaces(f0/0.1 and f0/0.2) under the same main interface? How does routers behave in this scenario?

not sure if you are talking about a router on a stick!

Yes, you can configure different MTU on different subinterfaces. Router checks the MTU from the main interface.

Yes, you can configure different MTU on different subinterfaces. Router checks the MTU from the main interface. If the main interface MTU is lower value than the MTU on the subinterface, the router changes the MTU on the main interface to match with the subinterface.

Yes we can, the router will be behave as if each sub interface independent from each other