The invention discloses a fuel cell system and a thermal management method thereof. The fuel cell system comprises a first circulating liquid path and a second circulating liquid path. A controller isconfigured to control the operation of the first or second circulating liquid path according to the temperature information detected by a first temperature sensor. The thermal management method includes: using the controller to determine whether the real-time temperature of an electrolyte is within an optimal temperature range: if so, controlling first and second reversing valves by the controller to operate the second circulating liquid path; if not, controlling the first and second reversing valves by the controller to operate the first circulating fluid path; if the real-time temperature is higher than a first threshold, using an energy storage heating device to absorb the heat of a circulating liquid; and if the real-time temperature is lower than a second threshold, using the energystorage heating device to heat the circulating liquid. Based on the double circulating liquid path structure design, the thermal management method effectively solves the problems of operation heat dissipation, low-temperature operation and low-temperature start of the fuel cell system, and has the advantages of high reliability, high energy utilization rate and low cost.