Gear tooth spalling is a typical tooth surface defects in gear transmission. The accurate calculation of the time-varying mesh stiffness of the gear pair with spalling defect under mixed elastohydrodynamic lubrication (EHL) plays an important role in tooth damage prediction and fault feature analysis. In this work, an improved time-varying mesh stiffness (TVMS) model of spalling faulty gear in mixed EHL line contact considering the coupled effect of rough surface topography is established. The proposed model considers the combined effect of spalling defect, surface roughness topography, and lubrication on the contact characteristics of the meshing interface to obtain a revised contact stiffness, which is further used to determine the comprehensive TVMS. The cylindrical contact coefficient for curved meshing interface with spalling fault is derived and incorporated into the statistical micro-contact Greenwood and Williamson model (GW model) to obtain the asperity contact stiffness. The revised contact stiffness at the rough faulty gear interface is obtained from the parallel action of the asperity contact stiffness and oil film stiffness under load-sharing concept. The dynamic responses of the gear system are analyzed using the established mesh stiffness model through the six degrees of freedom translational-torsional dynamic model, in which the dynamic meshing force is calculated iteratively using the transit surface topography and geometrical parameters along the line of contact instead of a quasi-static meshing force. Effects of multi-parameters as surface roughness, spalling fault size, and lubricant on the mesh characteristics and dynamic responses of the gear system are further investigated and discussed.