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Autonomous decentralized control system based on FPGA based hardware controller is proposed. Progress of FPGA technology makes it possible to include the software macro CPU core into the FPGA chip, a high flexibility can be realized for the construction of the control processor in power electronics application. In the proposed method, all the control system is implemented in one FPGA chip. Complicated calculations are assigned to hardware calculation logic, and the parallel processing circuit makes it possible to realize minimizing the calculation time. Also Nios II CPU core is implemented in the same FPGA chip, and the software development can be applied for non-time critical calculations. Two parallel connected UPS system was constructed and load sharing characteristics were verified through simulations and experiments.