Plastoelastohydrodynamic lubrication of rough surfaces (R-PEHL) is a cutting-edge area of research in interface fluid-structure coupling analysis. The existing R-PEHL model calculates the elastic-plastic deformation of rough surface by the Love equation in a semi-infinite space smooth surface, which deviates from the actual surface. Therefore, it is an innovative work to study the exact solution of elastic-plastic deformation of rough surface and its influence on the solution results of R-PEHL model. In this paper, a new contact calculation model of plastoelastohydrodynamic lubrication (PEHL) with three-dimensional (3D) rough surface is proposed by integrating numerical method of EHL and finite element method. The new model eliminates an original error introduced by the assumption of semi-infinite space in contact calculation, providing wide applicability and high accuracy. Under the given rough surfaces and working conditions, the study reveals that: (1) the oil film pressure calculated by the new model is lower than that of the smooth surface in semi-infinite space by 200–800 MPa; (2) the Mises stress of the new model is 2.5%–26.6% higher than that of the smooth surface in semi-infinite space; (3) compared with the semi-infinite space assumption, the rough surface plastic deformation of the new model is increased by 71%–173%, and the local plastic deformation singularity may appear under the semi-infinite space assumption; (4) the plastic deformation caused by the first contact cycle on the rough surface of the new model accounts for 66.7%–92.9% of the total plastic deformation, and the plastic deformation of the semi-infinite space accounts for 50%–83.3%. This study resolves the contradiction between the smooth surface assumption and the rough surface in the existing R-PEHL model, establishing a solid logic foundation for the accurate solution of R-PEHL model.