The invention discloses a semiconductor packaging method of wafer level silicon-based through hole, belonging to the field of semiconductor packaging. The packaging method substantially comprises the following steps: 1, making a cavity structure on a cover plate; 2, bonding the front surface of the cover plate with the front surface of a wafer through a bonding machine; 3, grinding the rear surface of the wafer by a grinder, and implementing a stress plasma etching on the rear surface of the wafer; 4, removing all silicon belonging to a scribe line region starting from the rear surface of the wafer; 5, etching the rear surface of the wafer in order to form silicon through holes, and exposing a bonding pad; 6, making passivation layers, metal layers and solder mask layers sequentially in the rear surface of the wafer and the silicon through holes, so as to compose a redistributed circuit layer, thereby conducting the solder pad to a designated solder ball position on the rear surface of the wafer; 7, making solder balls and cutting along the scribe line. By the implementation of the semiconductor packaging method of wafer level silicon-based through hole, the yield rate of wafer cutting technique is increased, the stress level in package structure is reduced, and the boundary dimension of the package structure is decreased.