Based on the three-dimensional (3D) finite element method (FEM) and Taguchi method (TM), this paper analyzes the tooth surface contact stress (TSCS) of spur gears with three different influence factors: tooth profile deviations (TPD), meshing errors (ME) and lead crowning modifications (LCM), especially researching and analyzing the interactions between TPD, ME and LCM and their degree of influence on the TSCS. In this paper, firstly, a 3D FEM model of one pair of engaged teeth is modeled and the mesh of the contact area is refined by FEM software. In the model, the refined area mesh and the non-refined area mesh are connected by multi-point constraint (MPC); at the same time, in order to save the time of the FEM solution on the premise of ensuring the solution’s accuracy, the reasonable size of the refined area is studied and confirmed. Secondly, the TSCS analyses of gears with one single influence factor (other factors are all ideal) are carried out. By inputting the values of different levels of one single factor into the FEM model, especially using the real measurement data of TPD, and conducting the TSCS analysis under different torques, the influence degree of one single factor on TSCS is discussed by comparing the ideal model, and it is found that when the influence factors exist alone, each factor has a great influence on the TSCS. Finally, through TM, an orthogonal test is designed for the three influence factors. According to the test results, the interactions between the influence factors and the influence degree of the factors on the TSCS are analyzed when the three factors exist on the gear at the same time, and it is found that the TPD has the greatest influence on the TSCS, followed by the lead crowning modified quantity. The ME is relatively much small, and there is obvious interaction between ME and LCM. In addition, the optimal combination of factor levels is determined, and compared with the original combination of a gear factory, we see that the contact fatigue performance of the gear with the optimal combination is much better. The research of this paper has a certain reference significance for the control of TPD, ME and LCM when machining and assembling the gears.