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In order to improve the design success rate, shorten the development cycles and reduce the cost , a new algorithm based on FDTD is presented to modify the simulation model in the design of high-speed PCB. Through the simulation model of signal integrity, the simulation error in the design caused by the defect of the unmodified model is analyzed. By comparison of the waveform before and after modified, the efficiency of this algorithm is verified. The algorithm can not only improve the accuracy of the simulation model significantly, but also has excellent portability. It can be easily combined with the commercial software, and then the modification of the simulation model is achieved automatically.