The interfacial bonding performance between epoxy resin and concrete is one of the key factors affecting the effect of fiber-reinforced concrete structures, and the carbonation of concrete affects the interfacial bonding performance between epoxy resin and concrete. The effect of carbonation on the interfacial bonding performance between epoxy resin and concrete was investigated based on molecular dynamics. The research results show that the existence of carbonation can enhance the interfacial bonding performance between epoxy resin and concrete. The distribution of epoxy resin is closer to the concrete surface, and the interaction energy between epoxy resin and the substrate is higher. Static structure analysis shows that epoxy resin and concrete substrate are mainly connected by calcium oxygen bond and hydrogen bond, and the number of chemical bond connections on the calcium carbonate surface is more and the chemical bond strength is higher. Dynamic analysis shows that the surface of calcium silicate hydrate is bound by fewer ion pairs and hydrogen bonds, and epoxy resin can move freely, which is not beneficial to strong interfacial bonding performance.