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In order to reduce the number of control instructions DSP issued and the consuming time of PMD compensation, an algorithm processing and logic control unit for first-order and second-order PMD compensation is designed. It plays the functions of DSP's algorithm processing and FPGA's logic control adequately. The configuration of the unit, detailed hardware design and experiment result are also given in the paper. The average consuming time of the unit is even shorter than that of existing DSP compensation module. And it has a better compensation effect.