Your father may think you are tending towards scruples or towards an overzealous and unhealthy piety.
You are a minor under the care of your parents, so you should listen to your father and refrain from going twice a day for now. Talk to him to understand his reasons. But, you should do as he asks.
You can also talk to your pastor about your habit of going to two daily masses each day, and examine what may be the impetus behind doing that-- why are you going to mass and then turning around and going again just 3 or 4 hours later? It’s not bad, but as your father said it is also not necessary and if you are feeling a compulsion to do it then it may be harmful to your spirituality.
We cannot know all these details and the dynamics of your relationship with your father, etc, so these are just some things to think about.
Ultimately, yes, be obedient to your father in this. If you want to revisit it at a later time, do so. Once you are older, you can make your own choices.