A coupled discrete element model for two degree of freedom subgrade and pavement was established in this paper to study the settlement problem caused by the red beds filling material in the Lanzhou-Haishiwan section of the G6 Beijing-Tibet Expressway. Through iterative calculation, the meso parameters of each layer of the material were obtained. The Fish function was compiled, and the impact load and half sine load were used to simulate the traffic load. On this basis, the displacement and stress time history curves of the subgrade and pavement under traffic load were analyzed. Research results show that displacement stratification occurs at the interface between the base layer and the red layer filler, and the base layer, subjected to horizontal tensile stress, is a high risk area for crack development. Therefore, there should be regular monitoring for cracks in this area during periods of highway operation. The PFC model realizes cooperative deformation coupling of subgrade soil and pavement structure layer in the discrete element software, provides a research idea for road disease problems and settlement deformation calculations in poor subgrade areas, and lays a theoretical foundation for subsequent subgrade disease remediation in this area.