Understanding the underlying processes associated with the thermo-oxidative performance of the ethylene-propylene-diene monomer (EPDM) is essential for assessing and improving its waterproofing performance in underground infrastructures. To explore the fundamentals of EPDM degradation behavior during thermal oxidation, this paper investigates the effects of hydrocarbon free chain, carbon crosslink, chain scission, hydroxyl, and ether crosslinks, on its kinetics and mechanical properties through molecular dynamics (MD) simulations. Several EPDM thermo-oxidative models were built and verified by comparing the simulation results of oxygen diffusivity, glass transition temperature, and mechanical properties with reported experimental ones. Then the radius of gyration, free volume, density, transport, glass transition, and uniaxial compression performance were investigated via MD simulations. The results show that crosslinking in the thermal oxidation process has a significant influence on the free volume, glass transition temperature, and mechanical properties of the system; the hydroxyl and chain scission mainly interfere with the transport properties; all of these affect the structural conformation.