The work aims to analyze various kinds of factors affecting simulation results through simulation of compression and cushioning performances of molded pulps with bi-wave structure in finite element method. Bi-wave structure of molded pulps was designed. The samples were prepared and the cushioning performance was tested. The finite element model was constructed and the model reliability was verified, based on which the effects of mesh quantity and the change in friction coefficient, material model, elasticity modulus and Poisson’s ratio on the simulation results were respectively discussed. The simulation results of bi-wave structure of molded pulps were greatly affected by the classification of mesh quantity and the change in Poisson’s ratio, material model and elasticity modulus, while such results were less affected by the change in friction coefficient. Before finite element analysis, test of irrelevant of mesh to the model should be conducted. The material model should be isotropic. The load during the static compression will increase with elasticity modulus and Poisson’s non-linearly.