Abstract: Freshwater lens is an important groundwater resource in an island, and plays a key role in meeting the needs of people's daily life and maintaining the ecosystem of the island. At present, the dune area of the Yongxing Island increases by 50%. In order to examine the impact of geomorphologic changes on freshwater lens in the island, a 3D mathematical model of the freshwater lens is constructed using the SEAWAT module in the GMS software. Sensitivity analysis of some parameters is also carried out. The results show that the infiltration coefficient of precipitation has the greatest influence on the thickness of freshwater lens, followed by the hydraulic conductivity and specific yield. With the existing topography unchanged, the freshwater lens of the Yongxing Island will reach a stable state in about 25 years. At that time, the maximum thickness of the freshwater lens will increase from the previous 14 m to 17.5 m, and the calculated freshwater reserves is about 328×10⁴ m³. This paper presents a numerical model for examing the effect of geomorphologic changes on the freshwater lens, which has important theoretical significance and practical value for the further exploitation and management of freshwater resources in the Yongxing Island and other similar islands.