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A fuzzy controller based on improved Generalized-Membership-Function(GMF) algorithm for a fuel cell generation system was introduced. Under the demands on control in application of the converter, a Field Programmable Gate Array (FPGA) realization method to manage the power flow was given. This control system based on the proposed modified GMF was proved to be a universal approximation system in theory. The fuzzy control technique was combined with Eletronic Design Automatic(EDA)technique and a paralleling fuzzy controller was implemented in FPGA. Paralleling fuzzy controller based on improved GMF algorithm was implemented on a Cyclone FPGA. The result of simulation based on QuartusⅡ confirmed the validity of the proposed method.