With molecular dynamics simulations, we calculate the probability as well as the angle and energy distributions when the reflection and resputtering of Mo/Si atoms occur. Four types of collisions are considered: Mo-on-Mo, Mo-on-Si, Si-on-Mo, and Si-on-Si. We find that the lower the amount of energy transferred to the substrate is, the more likely it is for reflection to occur, but the less likely for resputtering. Moreover, the effect of incident angle on the reflection and resputtering probabilities is related to the types of sputtered atoms and substrate atoms. However, the higher the incident energy is, the higher the reflection and resputtering probabilities are. Finally, by the magnetron sputtering experiment, we fabricate the Mo/So multilayer samples on substrates with different inclination angles, and the experimental result verifies the simulation result. This study should be helpful in simulation of magnetron sputtering deposition and the optimization of deposition process.