To address the issues of the brittleness, low tensile strength, insufficient bond strength, and reduced service life associated with ordinary cement concrete being used as a repair material, a water-based epoxy (WBE) and carbon-nanofiber-reinforced concrete composite repair material was designed, and the mechanical properties, bonding performance, and durability of the concrete modified using WBE and carbon fiber under various WBE contents were investigated and evaluated. In this paper, a self-emulsifying water-based epoxy curing agent with reactive, rigid, flexible, and water-soluble chains was obtained via chemical grafting, involving the incorporation of polyethylene glycol chain segments into epoxy resin molecules. The results demonstrated that a WBE has a contributing effect on improving the weak interfacial bond between the carbon fiber and concrete; moreover, the composite admixture of carbon fiber and WBE improves the mechanical properties and durability of concrete, in which the composite admixture of 1% carbon fiber and 10% WBE has the best performance. The flexural strength and chlorine ion permeability resistance of concrete were slightly reduced after more than 10% admixture, but bond strength, tensile strength, compressive strength, dry shrinkage resistance, and frost resistance were promoted. The addition of WBE significantly retards the cement hydration process while greatly improving the compactness and impermeability of the concrete. Furthermore, the combined effects of WBE and carbon fiber effectively prevented the generation and expansion of cracks. The interaction mechanism and microstructure evolution between the WBE, carbon fiber, and cement hydration were described by clarifying the mineral composition, organic–inorganic interactions, the evolution of the hydration products, and composite morphology at different scales. Carbon fiber and WBE exhibited synergistic effects on the tensile strength, ductility, and crack resistance of concrete. In the formed three-dimensional network structural system of concrete, the WBE formed an organic coating layer on the fiber surface and provided fiber protection as well as interfacial bonding reinforcement for the embedded cement particles.