Low frequency vibration induced by the operation of subway train has been widely concerned by people, and it is of great significance to the research of low frequency vibration control. This study establishes a three-dimensional dynamic finite element model for rail-tunnel-stratum utilizing a moving excitation force function to simulate the interaction forces generated by wheel-rail contact. The core idea of this paper is to reduce low frequency vibration by reducing energy transfer density in the stratum. Firstly, the dynamic response law of ground and surface induced by subway train operation is analyzed to reveal the propagation and attenuation mechanism of low frequency vibration. Then, through two different track types of ordinary integral track bed and steel spring floating slab track, the effects of tunnel lining parameters and track bed parameters on low-frequency vibration of the ground surface in ordinary integral track are systematically analyzed, and the steel spring floating slab track is optimized to increase the stiffness and thickness of the bottom board. The control effects of optimized bottom board parameters and isolator arrangement on low-frequency ground surface vibration are studied. The calculation results show that the low-frequency part decays slowly in both stratum and surface with the increase of the distance from the longitudinal axis of the tunnel. The stiffness and height of track bed and the stiffness of tunnel lining have great influence on the low frequency vibration, but the thickness of tunnel lining has little effect on low frequency vibration. With the increase of the stiffness and length of the bottom board, the control effect of low frequency vibration becomes better, the fewer the number of isolators, the better the control of low frequency vibration.