Nano molding technology (NMT) has shown great potential in the preparation of metal/resin composites, which can integrate resin and metal into a lightweight, high-strength metal matrix composite. However, due to the poor interfacial bonding strength between metal and polymer, the application of the metal/polymer composites is limited. In this paper, we proposed a novel method to improve the bonding strength between Fe–Co–Ni alloy and epoxy resin by Nano Perfusion Technology (NPT), featuring in situ growth of carbon nanotubes (CNTs) in the pores on anodized Fe–Co–Ni alloy porous surface, followed by a perfusion of epoxy resin throughout the pores that had been in situ grown CNTs. Due to the “anchor effect” of CNTs, the bonding strength between the epoxy and the alloy matrix is improved. The results showed that the interfacial bonding between the in situ CNTs-modified alloy and the resin was significantly improved compared to the metal-resin composites surface treated with T-treatment in traditional method of NMT. The maximum interfacial bonding force of the alloy-CNTs/epoxy composite reached up to 691.80 N, which was 460, 315, and 267% higher than those by mechanical treatment, without CNTs and T-treatment, respectively. This work provides a new approach to protect metals or alloys from environmental corrosion, impact damage, and so on.