The answer, says Honolulu Community College Professor Richard Brill, is elementary.
Heat is a form of energy and hot molecules are energetic molecules.
So, the more energy they have, the hotter the temperature. In conventional ovens, Brill says heat is transferred from the air to food by collisions of hot, energetic air molecules with colder, less energetic food molecules. This happens at the surface of the food. The inside of the food is then heated by conduction as the hotter, molecules near the surface collide with the molecules inside. Microwave ovens are a type of radio wave, just like the waves from a radio station travel through the air and shake electrons in an antenna, microwaves shake water molecules in food.