The present invention provides a multilayer structure filtering antenna and a microwave communication system. The multilayer structure filtering antenna comprises a first dielectric substrate, a second dielectric substrate and a third dielectric substrate which are overlapped from down to up; the lower surface of the first dielectric substrate is provided with a microstrip feeder; the lower surface and the supper surface of the second dielectric substrate are respectively provided with a first metal layer and a second metal layer, an entirety formed by the first metal, the second dielectric substrate and the second metal layer is provided with a plurality of metallization through holes in rectangular arrangement mode, the first metal layer, the second metal layer and a plurality of metallization through holes commonly form a rectangular resonant cavity, the first metal layer is provided with a coupling slot, and the second metal layer is provided with two opposite radiation slots; and the third dielectric substrate comprises a rectangular main body portion and two extension bodies, and the main body portion is provided with a radiation metal layer. The multilayer structure filtering antenna and the microwave communication system realize high-frequency selectivity, high gain and bandwidth improvement effects, solve the problem that the whole gain of the antenna id decreased caused by a non-radiation resonator, and realize assembling of a filtering antenna through the antenna itself.