The invention provides a control system and a control method of a fuel cell range extender and belongs to the technical field of new energy electric vehicles. A power cell is taken as driving energy, a fuel cell is taken as auxiliary range extending energy, in efficiency and the power ranges of the power cell, times of start of the fuel cell range extender are reduced to the greatest extent, damage to the range extender due to frequent start and the effect caused by frequent charge and discharge of the power cell on the service life are reduced, after the energy of the power cell is utilized greatly, the fuel cell is started, the output power of the fuel cell is controlled according to the required power, and the driving range is extended. According to the control system and the control method, the operating efficiency of the fuel cell and the power cell is optimized, the problems of the short driving range of the power cell and the high cost of the fuel cell are solved, meanwhile, service lives of the power cell and the fuel cell are prolonged, and the power property and the economic efficiency are unified efficiently.