Basalt fiber reinforced polymer(BFRP) with silica-alumina component, is always used in the harsh environment such as moist or corrosive environment，and water molecules will lead to the decline of the bonding capacity between epoxy resin and basalt fiber，which will further affect the mechanical properties and durability of BFRP. An aluminum-doped silica substrate model of basalt fiber surface is established by partly replacing silicon atoms with aluminum atoms. The evolution of interfacial bonding properties between epoxy and aluminum-doped silica substrate in water environment are simulated based on molecular dynamic (MD). Simulation results show that the bonding force of aluminum-doped silica substrate with epoxy is weaker than that of pure silica substrate. The epoxy and fiber substrate are bonded in the manner of H-bonds formed by oxygen of epoxy-hydrogen of substrate-oxygen of substrate. Water molecular weakens the bonding capacity by occupying the reactive sites of atomic pairs in H-bond. The feasibility of the molecular model was verified by the 47.53% decreased bonding force at the interface between basalt fiber bundles and epoxy resin under the condition of water immersion for 28 days.