The invention discloses a method for manufacturing a shallow junction complementary bipolar transistor. The main technological steps of the method are as follows: 1) forming an SOI material chip by the methods of silicon/silicon bonding, thinning and polishing; and 2) manufacturing the shallow junction complementary bipolar transistor by using the methods of deep-trench etching, deep trench isolation with polysilicon backfilling and a shallow isolation wall and combining with a longitudinal NPN pipe with a shallow junction polysilicon emitter and the complementary bipolar technology which is compatible with the longitudinal PNP pipe. The method improves the pressure resistance (BVCEO is greater than 5.0V) and the Early voltage of the complementary bipolar transistor and simultaneously takes into consideration of the characteristic frequency. The method greatly reduces the drain current of an isolation junction, and the drain current of the shallow junction complementary bipolar transistor is smaller than 10A. The method can be widely applied in the field of manufacture of high-speed complementary bipolar technologies.