Combining self-heating effect, mobility degradation in high electric field and avalanche generation effect, a two-dimensional electro-thermal model of the typical silicon-based n+-p-n-n+ structure bipolar transistor induced by high power microwave is established in this paper. By analyzing the variations of device internal distributions of the electric field, the current density and the temperature with time, a detailed investigation of the damage effect and the mechanism of the bipolar transistor under the injection of 1GHz equivalent voltage signals from the base and collector is performed. The results show that temperature elevation occurs in the negative half-period and the maximum temperature falls slightly in the positive half-period when the signals are injected from the collector. Compared with the former, device damage occurs easily with the signals injected from the base. Specifically, the base-emitter junction is susceptible to damage. The damage results caused by two large-amplitude signals with initial phases of 0 and respectively indicate that the injected signal with an initial phase of is liable to cause device damage. Meanwhile, the emitter series resistance can enhance the capability of the device to withstand microwave damage effectively.