The invention provides a microwave multi-chip packaging structure using a silicon through hole and a manufacture method thereof. The method uses a temperature safety valve (TSV) to achieve two-sided integrated system-stage packaging structure, when a monolithic microwave integrated circuit (MMIC) chip needs integrating, a user does not need embed a substrate before wiring, and performance, reliability and rate of finished products of the packaging structure are improved. Simultaneously, processes such as injection, corrosion, release and high temperature annealing in a manufacture process can be used before integration of the MMIC, and components needing special processes can be assembled and integrated in advance on the other side of the substrate. Therefore, the substrate comprising active and passive devices, micro-electromechanical systems (MEMS), photoelectric devices and the like can be conveniently manufactured in a large scale before integration of the MMIC, and the manufacture method is simple in process, reduces cost, and is advanced and reliable at present.