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The Pan-Boolean algebra logical control method is used as decreasing the roof whiplash effect of ship lifting under the earthquake. In accordance with the vibration control experience of ship lifting structure, we establish the different Pan-Boolean algebra logical control rules and designing 9 points, 25 points and the 27 points Pan-Boolean algebra logical controller separately, which is applied to the existing ship lifting system of MR intelligence. The control effect and serviceability of the different Pan-Boolean algebra logical controller was analysed by MATLAB/Simulink. The simulation results show that the more division of the movement process would realize the system's anticipated performance better, and by which the seismic whipping effect of ship lifting under the earthquake is significantly mitigated.