Objective Finite element modeling was commonly used in biomechanical evaluating and optimizing of the patient-specific interbody fusion cages. However, it was a time-and labor-intensive process and relied on the researcher's experience. The purpose of this study was to investigate the effects of the modeling parameters on the simulation results in evaluating and optimizing the patient-specific interbody fusion cages with the finite element (FE) models. Methods Biomechanical assessment of L3-L4 spinal cage was used as an example. Six modeling parameters were taken into consideration: the element type of ligament, the size of mesh, the thickness of cortical outer shell, the definition of the cancellous bone material, the friction coefficient of thefacet joint, and the connection style between the vertebral bone and the cage. According to orthogonal experimental design, 18 FE models were built to analyze the influence of these parameters on the simulation results. Results The element type of ligament, the friction coefficient of the facet joint, and the connection style between the facet bone and the cage affected the simulation results significantly when the maximum von Mises stress on the cage was taken as the evaluating indicator; the element type of ligament, the connection style between the vertebral bone and the cage affected the simulation results significantly when the maximum deposition distance of the cage was taken as the evaluating indicator. The size of mesh, the thickness of cortical outer shell, and the definition of cancellous bone material did not affect the simulation results significantly. Conclusions The method proposed in this study finds out 3 parameters (the element type of ligament, the friction coefficient of the facet joint, and the connection style between the facet bone and the cage) affect the simulation results significantly during evaluating biomechanical performance of interbody cage with the finite element analysis. This method can also be used for optimizing the finite element modeling process during evaluating other patient-specific implants.