The invention discloses a heating system for starting a fuel cell at a low temperature with air backflow and a heating method thereof. The system comprises an air filter, an intakeport flowmeter, an intakeport tee, an air pump, a humidifier, an inlet flowmeter, a fuel cell stack, an outlet tee, an air flow controller, a temperature sensor and a controller. When the heating system provided in the invention works, heat-containing air compressed by the air pump heats an air reaction interface and other battery assemblies of the fuel cell stack, and then a part of or all the air tail gas of the fuel cell stack flows back and passes through the air pump through controlling of the flow controller so as to cyclically heat the air reaction interface and the other battery assemblies of the fuel cell stack. According to the invention, air tail gas containing waste heat of the air pump is cyclically used to heat the air reaction interface of the fuel cell stack, so melting of ice crystals on electrodes is accelerated, mass transfer of fuels and proton transfer are smoothly carried out, starting of fuel cells with a temperature lower than 0 DEG C is accelerated, and energy consumption of a storage battery used as an auxiliary power supply can be saved.