The epoxy resin composed of bisphenol A diglycidyl ether (DGEBA) and methyl tetrahydrophthalic anhydride (MeTHPA) has been found to enhance its thermal conductivity by increasing its molecular weight and crosslinking density. This was achieved through experiments and all-atom molecular dynamics simulations. Molecular dynamics was employed to calculate the root-mean-square displacement, free volume fraction, potential energy, density, and quantity of hydrogen bonds. The results showed the influence of molecular weight and crosslinking density on the system's thermal conductivity. The results showed that the high molecular weight epoxy resin system exhibited high thermal conductivity at elevated crosslinking densities. During the crosslinking process, the epoxy resin's thermal conductivity increased, starting with the center portion weakening and then strengthening. In addition, a simulation-verified free volume was found to have an inversely proportional connection with thermal conductivity. This study explored the thermal conductivity mechanism of epoxy resin by analyzing the structural changes at the micro level and correlating them with the changes in thermal conductivity at the macro level to enhance guidance for industrial production and practical application.