With the rapid pace of urbanization, global demand for concrete is increasing, shifting focus from construction to repair and maintenance. Traditional cement-based repair materials generally suffer from brittleness and poor durability, failing to meet the growing demand for durable repair solutions. We developed a water-oil gradient composite epoxy resin (CEP) modified cement-based repair mortar (MCEP) using self-synthesized water-based epoxy resin (WEP) and oil-based epoxy resin (EP). Durability tests showed that CEP-modified cement mortar exhibited improved resistance to solution penetration, shrinkage, acid corrosion, and freeze-thaw cycles, with increased CEP content positively affecting mortar durability. Notably, the addition of CEP not only enhanced the interface bonding strength between MCEP and old concrete but also maintained good bonding stability under moisture erosion. X-CT and SEM microstructural tests revealed that CEP is evenly distributed in the cement paste, forming a cement-polymer interpenetrating network structure, which improves crack resistance and reduces solution penetration in MCEP. Molecular dynamics simulations explored the adsorption of CEP on calcium aluminate hydrate (AFt), a key cement hydration product, and the moisture transport mechanisms in AFt and CEP-modified AFt nanopores. Results indicated that CEP molecules adsorb onto AFt via ionic and hydrogen bonds, demonstrating good stability. During moisture penetration, CEP reduced water transport efficiency in the nanopores. CEP modification improved the crack resistance and durability of cement repair mortars, providing valuable insights into molecular-scale enhancements in water permeability resistance. This study aims to contribute to the design and practical application of water-oil gradient epoxy resins and other polymer-modified cement-based repair materials.