The invention relates to an energy flow controller for fuel battery electric motor car, and the controlling system is composed of pedal, entire controller ECU, fuel battery engine, nickel hydrogen battery package and driving system. The invention is to implement reasonable distribution of energy source between fuel battery and fuel storage battery and enhance and optimize power performance of the whole car. Its character: there is also an energy flow controller connected between the ECU and the driving system, where the energy flow controller is a module in the ECU, its input end is connected with the output end of a fuzzy logic controller (FLC), and its output end is connected with the input end of an electric motor controller in the driving system. It synthesizes advanced techniques in the fields of CAN field bus, fuzzy control, communication, etc.