Freshwater resources on small coral islands mainly exist in the form of freshwater lenses. The freshwater lens is highly vulnerable to salinization due to natural recharge variations and urbanization construction. However, it is unclear how a freshwater lens evolves under the influence of urbanization construction and which factors control its evolution. Based on the hydrogeological data of a small coral island in China, a corresponding 3D numerical model was established by the Visual MODFLOW software to investigate the formation and evolution of freshwater lenses under natural conditions. Thereby, the island reclamation scenario and impermeable surface scenario were set up and the changes in morphology and volume of the freshwater lens were analyzed. The results show the following: (1) After island reclamation and island building, the freshwater lens would reach a stable state after 25 years and the freshwater lens would also appear in the newly added part of the island with a thickness of 9.5 m, while the volume of the total freshwater lens would increase to 1.22 times that of the original island. (2) When the impermeable surface is built at different positions of the island, the reduction in the volume of the freshwater lens, in the order from large to small, is Scenario B (northeast side), Scenario A (southwest side) and Scenario C (central); with the increase in the impermeable surface area, the volume of the freshwater lens would gradually decrease and the volume of the freshwater lens would decrease by more than 50% with the impermeable surface exceeding 30% of the island area. The study has important implications for the conservation and rational development of subsurface freshwater resources on islands.