The permeation of marine water can lead to severe degradation of the protective properties of polymer composite coatings. At present, experimental studies on the anticorrosive and mechanical properties of polymer composite coatings are relatively mature, but the impermeability and mechanical property changes of the coating during the permeation process are challenging tasks to be studied only by experiments. In this paper, molecular dynamics (MD) models of composite coatings consisting of pure epoxy resin (EP), graphene/epoxy resin (Gr/EP), and graphene oxide/epoxy resin (GO/EP) were constructed respectively. MD simulations were performed to reveal the impermeability and mechanical property changes of composite coatings from an atomic perspective. The results show that GO has strong interfacial interaction with EP and the best effect to enhance the impermeability and mechanical properties of epoxy coatings. NaCl solutions can damage the coating microstructure and occupy the Gr and GO surfaces, causing them to no longer have an enhancing effect. The study of GO/EP coatings with different permeation degrees shows that the mechanical properties of the coating decrease as the penetration degree increases.