I am trying to make a simple flag animation with Blender then export it to Unity3D. I already made the flag in blender with a wind force and the flag works well in Blender. However I am not sure how to create an animation out of the flag with the wind force and export that animation to Unity3D.
You can't. Unity has its own cloth simulation tools, but you can't import any simulation from Blender. This is true for smoke, cloth, soft body, rigid body, fluid, etc. In general, if it isn't a mesh or directly related to a mesh (e.g., UV maps), Unity will have nothing to do with it.