The EHL model of water-lubricated structure was numerically calculated by using the Finite element coupling algorithm. Under the consideration of elastic deformation of the rubber liner, numerical simulations of pressure distribution, thickness of water film and friction characteristics were theoretically performed with different values of elastic modulus and thickness of the liner. The results revealed a strong domination of elastic deformation in the EHL performance, which is more obvious at higher values of elastic modulus and thickness of the liner. With the decrease of elastic modulus of rubber liner, the water film thickness becomes larger on both the circumferential and axial directions, and the pressure values of water film decrease. Then, the effective area of pressure is expanded, and the effects of EHL become better. Consequently, the friction and wear of the water-lubricated structure are weakened. Within certain extent, the effects of decreasing the value of elastic modulus of rubber liner and increasing the value of thickness are equivalent on enhancing the EHL performance of water-lubricated structure.