Simulations based on molecular dynamics and mesodyn theories were used to investigate the compatibility, morphology evolution of polypropylene/polycarbonate (PP/PC) blends, and the relationship between the composition and microstructure. Results of FloryHuggins interaction parameters, integral structure factor, X-ray intensity, free-energy density, and order parameters all indicated that phase separations occurred in all PP/PC blend systems, and poor compatibility was exhibited for this polymer pair. The systems of PP/PC = 54/46, PP/PC = 31/69, and PP/PC = 18/82 showed stronger immiscibility and the faster separation process, while the systems of PP/PC = 82/18 and PP/PC = 5/95 showed less immiscibility and a slower separation process. Compared with the results of mechanical properties tests, the appearance of a cocontinuous structure obtained from simulation corresponds to the transition point of impact strength and tensile strength. After transition, the mechanical properties of the blends depended on the properties of the PC matrix, and the impact strength and tensile strength were both clearly enhanced. As the simulation steps increased, the morphology of PP/PC = 54/46 blend developed into a double-lamellar structure by coarsening of PC phase from initial homogeneous configuration. In addition, the compatibilizing effect of SEBS was also investigated at the microscale, and varying the content of PS block in SEBS has little effect on the morphology of blend.