The acceleration and deceleration movement of the metro near the metro station have a certain impact on the foundation soil. After the soil has been sloped and sampled, a dynamic three-axis undrained dynamic test is conducted to study the influence of the distance of the metro station, acceleration, dynamic stress amplitude, and consolidation confining pressure on the cumulative plastic deformation of saturated soft clay. The results show that the cumulative plastic strain curve of soft clay at variable frequency cyclic loading in and out of the station can be roughly divided into three stages: explosive growth, rapid growth, and gradual stability. The increase in the distance from the metro station, the increase in the amplitude of the dynamic stress, and the decrease in the consolidation confining pressure can reduce the number of entry and exit times required for the soil to enter the gradual stabilization phase, increase the vertical deformation of the soil, and reduce the shear deformation. As the acceleration value in and out of the station increases, the vertical deformation of the soil decreases but the shear deformation increases. For the actual project, the initial stage of metro operation, the settlement deformation of the soil in the inbound section, the horizontal displacement of the soil in the outbound section, the horizontal displacement under the larger acceleration condition, the settlement under the smaller acceleration condition, the high dynamic stress amplitude, and the soil area with a low consolidation stress are the focus of engineering geological disaster prevention.