The invention discloses a thermal management system for low temperature starting of a fuel cell power generation system and a method thereof. The thermal management system comprises an internal circulating heating system and an external circulating cooling system. The internal circulating heating system is composed of a fuel cell stack, a fuel cell stack cooling liquid outlet sensor, an outlet tee, a water tank, a heater, an internal circulation pump, an internal circulation one-way valve, an inlet tee, and a fuel cell stack cooling liquid inlet sensor. And the external circulating cooling system consists of the fuel cell stack, the fuel cell stack cooling liquid outlet sensor, the outlet tee, the water tank, an external circulation pump, a radiator, an external circulation one-way valve, the inlet tee, and the fuel cell stack cooling liquid inlet sensor. By adding an internal circulating heating system, the system of the invention solves the heat radiation problem of the fuel cell stack, and simultaneously can rapidly raise the temperature of the fuel cell stack, which can be always maintained in an optimal working temperature range. Thus, the performance of the fuel cell can be maintained in a most stable state, and the service life can be prolonged.