The cross-linking structure of the Ethylene-propylene-diene monomer (EPDM) is made up of a number of cross-linking types, including carbon atoms from the main chain or monomer and ether crosslinks formed during degradation. Through molecular dynamic simulations, the contribution of each type of cross-linked structure to the dynamics and mechanical properties of EPDM, the study's focus, were investigated. Cross-linking between the tertiary carbons of two main chains, cross-linking at the monomer's unsaturated position, ether cross-linking after oxidation, and other combinations of target cross-linked carbon atoms from different positions, totaling eight types of cross-linked types, were mixed with EPDM free chains in a 1:1 ratio to form eight types of cross-linked EPDMs. These varieties of cross-linked EPDMs were then compared to an uncross-linked EPDM in terms of density, radius of gyration, free volume, mean square displacement, and uniaxial tensile stress-strain curves. It was found that the cross-linking was always proven to have a favorable influence on mechanical characteristics; however, the relaxation inhibition effect varied. The cross-linking between the diene monomer at the C9 position resulted in a more flexible molecular shape and was more than double the free volume of the uncross-linked EPDM, resulting in an improved diffusion ability. The ether cross-linking produced by the oxidation of the side chain cross-linking improved the positive contribution to stiffness and enhanced the inhibitory impact on diffusion properties, whereas the main chain cross-linking had the opposite effect. The research presented in this study leads to a better knowledge of the microscopic aspects underlying EPDM performance.