The oxidation mechanism of ultra-high-molecular-weight polyethylene (UHMWPE) and polyoxymethylene (POM) in hydrogen peroxide solution was investigated by molecular dynamics (MD) simulations via reactive force field (ReaxFF) method. MD results from ReaxFF suggested that UHMWPE provided better antioxidation activity at high temperature (>373 K) than its POM counterpart in the same concentration of hydrogen peroxide solution. Furthermore, POM was relatively more susceptible to erosion and swelling because of the infiltration of H2O2 solution. Calculations of the diffusion coefficient at different temperatures permit further understanding of the chemical phenomena involved in the level of oxidation in the course of MD simulations. Results of the simulations are generally consistent with the previous experimental available in literature. The simulations also provide new insights into understanding the mechanism resulting oxidation products among the interested polymers.