The interfacial wear between silicon and amorphous silica in water environment is critical in numerous applications. However, the understanding regarding the micro dynamic process is still unclear due to the limitations of apparatus. Herein, reactive force field simulations are utilized to study the interfacial process between silicon and amorphous silica in water environment, exploring the removal and damage mechanism caused by pressure, velocity, and humidity. Moreover, the reasons for high removal rate under high pressure and high velocity are elucidated from an atomic perspective. Simulation results show that the substrate is highly passivated under high humidity, and the passivation layer could alleviate the contact between the abrasive and the substrate, thus reducing the damage and wear. In addition to more Si-O-Si bridge bonds formed between the abrasive and the substrate, new removal pathways such as multibridge bonds and chain removal appear under high pressure, which cause higher removal rate and severer damage. At a higher velocity, the abrasive can induce extended tribochemical reactions and form more interfacial Si-O-Si bridge bonds, hence increasing removal rate. These results reveal the internal cause of the discrepancy in damage and removal rate under different conditions from an atomic level.