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Traditional testing methods of ship shaking isolation need heavy workload, which has low efficiency and large error. Simultaneously the jitter caused by interference cannot be solved effectively. In order to solve these problems, the principle of ship shaking isolation is analyzed, and the model based on gradient descent and least-squares filtering algorithm is built, the filtering algorithm based on gradient descent and least squares is proposed to filter the measured data, the automated testing of ship shaking isolation is realized through VC++ programming, and the analysis of automated testing under the condition of ship shaking is carried out. Compared to the results tested by traditional methods, the simulation results show that the filtering algorithm which shortens testing time and improves the testing accuracy of ship shaking isolation could filter out random errors in the measurement data effectively, and the jitter caused by interference is significantly decreased.