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Design concept of FPGA based hardware controller with HW/SW codesign for autonomous decentralized control UPS system 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. The advantages of the proposed system is discussed through simulations and experiments.