It is known that mesoscopic characteristics of rock materials have a significant effect on its macroscopic mechanical properties. Based on the electron micrograph of mesostructure of typical rock materials, a mesoscopic simulation model was established to investigate the shock compression behavior of rock materials with different mesostructures, such as particle morphology, porosity and water. Numerical studies of mesoscopic behaviors were conducted on rock materials during the compressive processes using ANSYS Autodyn software. We obtained the effect of particle morphology, porosity and water on shock compressive properties at mesoscale. The Hugoniot parameters of rock materials with different mesostructures were determined, which were further applied in the impact cratering process simulations. The results show that both the Hugoniot parameters at mesoscale and the results of cratering process simulation are in good agreement with existing experimental counterparts in the literature. It is found that the porosity and water content have an obvious negative effect on the shock wave propagation in rock materials. The Hugoniot parameters determined by the mesoscopic simulation are applied to predict dynamic responses of rock materials, which can effectively reflect the effect of particle morphology, porosity and water content on impact cratering.