In this paper, in order to study the equivalent simplified model of multi-layer vertical isolation structure under heavy load train vibration, the two degree of freedom simplified calculation model of the multi-layer isolated structure is presented based on the equivalent principle of the first two order frequency and the total axial force. Based on the theoretical analysis, the equations of motion of the multi-layer vibration isolation structure with four kinds of simplified models are derived. Through the numerical simulation of some structures, we can found that the stiffness of transverse beam has little influence on the vertical stiffness of the planar structure, also it is easy to found that the two degree of freedom equivalent method is effective for the vertical vibration isolation structure of 5–8 by comparing the structural responses of single particle model, parallel multi particle vibration model and layer model.