The invention discloses a radio frequency module three-dimensional stacking structure and a manufacturing method thereof. The radio frequency module three-dimensional stacking structure comprises a glass cap layer, a glass carrier layer, a glass transfer frame layer, a silicon-based carrier layer, a ceramic packaging layer and radio frequency chips. The glass carrier layer, the glass transfer frame layer and the silicon-based carrier layer are all provided with through holes and interconnection lines; the glass cap layer, the glass carrier layer, the glass transfer frame layer, the silicon-based carrier layer and the ceramic packaging layer are stacked and interconnected in sequence from top to bottom; and the radio frequency chips are located on the upper surface of the silicon-based carrier layer and the upper surface of the glass carrier layer, and are connected with circuit bonding pads on the carrier layer through lead structures. Through combination and stacking of high-density substrates made of various materials, the radio frequency module is better in performance and higher in density, and the integration process is simple, flexible, better in reliability and the like.