The goal of constructing artificial islands on coral reefs in China is to build ecological habitable islands. The seawater in the artificial islands is gradually replaced by rainfall infiltration, and the freshwater lens formed is an important water source supporting the island ecosystem. The double-layer geological structure is widespread in coral reefs in the South China Sea. Considering the fact that there exists a great large difference in the permeability coefficients obtained using different measurement methods, this study established numerical simulation models for a coral reef island in the South China Sea to simulate the seawater refreshing process. The results show that different permeabilities of the double-layer geological structure of the artificial islands have no obvious influence on the formation time of fresh water on the artificial islands. The permeability of the Holocene coral sand sediment is the main factor controlling the freshwater lens of the artificial reef. The volume of the forming freshwater lens decreases logarithmically with the increase of the permeability coefficient, and the volume of the freshwater lens decreases more significantly with the increase of the permeability of the Holocene sediment than the thickness of the freshwater lens. After the freshwater lens crossed the unconformity surface and entered the Pleistocene reef limestone, due to the sudden increase of the permeability coefficient of the aquifer, the freshwater lens expanded to the horizontal direction and formed the mustached-shape freshwater body in the reef limestone.