In order to understand the significance of stratum stratification characteristics during the formation of underground freshwater lens in the coral reef islands, the particle size distribution (PSD) of the samples drilled at various depths of a coral reef island in the South China Sea is analyzed. The zone and strata of the island are determined according to the PSD characteristics in the horizontal and vertical directions, respectively. The area of each zone is determined based on the range covered by each drilling, and the thickness of each stratum is determined by the thickness of the samples with similar particle size in each drill hole. The permeability of the strata is controlled by the PSD of different zones and strata of the loose layer above the reef limestone, while the vertical and horizontal permeabilities control the difficulty of formation of the underground freshwater lens, the total thickness of the freshwater lens, and the thickness of the transition zone. The numerical model is established by considering the total area of the island and the number of strata. Finally, the numerical results of chloride ion concentration characteristics in the groundwater at different times, horizontal positions and depths are obtained.