Based on the hydrogeological data of an island, the hydrogeological conditions of the study area were generalized, and the corresponding two-dimensional numerical model was established by using Visual MODFLOW. The formation and water storage capacity variation of the lens was simulated by changing the coverage area of the impervious surface. The simulation results show that the maximum thickness of the initial island freshwater lens is 15.6 m. After configuration of the impermeable surface, the freshwater lens is stable again after 15 years. The outline of the lens with impervious surface is concave inward, and the maximum thickness is reduced to 14.6.m, and the underground fresh water storage of the island is reduced by 20.23%. Sensitivity analysis of the four influencing factors of the fresh water lens shows that the aquifer specific yield has the greatest impact on the underground freshwater storage, and then follows the impact of precipitation infiltration intensity, permeability coefficient and impervious surface coverage.