Taking the effect of actual surface topography under elastohydrodynamic lubrication (EHL) conditions on the contact state of gear pairs into consideration, a combination model with the analytical sliced method and two-dimensional (2D) EHL model is proposed to characterize the three-dimensional (3D) meshing characteristics of spur gears. Firstly, the surface topology of gears is tested by a surface profiler, which reflects that the topography of tooth surface accords with fractal characteristics. Thus, by adopting the Weierstrass–Mandelbrot (W-M) fractal function, the gear surface is characterized. Secondly, the numerical 2D EHL model with fractal roughness is established, and distributions of oil film pressure (OFP) and oil film thickness (OFT) at different meshing positions are obtained. Finally, considering the different topography distributions in the direction of face width, time-varying mesh stiffness (TVMS) is calculated based on the analytical sliced method. Thus, the influence of 3D surface topography can be considered. The Hertz contact stiffness is substituted by the time-varying lubricating oil film stiffness (OFS). The influences of tooth surface topography and lubricant film characteristics on meshing characteristics are investigated. The results show that the 3D rough tooth surface may be well characterized by a fractal function with random phase. Moreover, there is a great difference in the distribution of OFP and OFT between rough and smooth surfaces, which certainly influences the gear meshing characteristics.