The formation and storage of fresh groundwater in coral reefs is affected by many factors. The permeability of porous media in island and reef formation is one of the main controlling factors. Coral sand is the only medium for the formation of coral reefs. Its permeability characteristics are very different from the permeability characteristics of quartz sand from land sources. In this study, a series of indoor model tests and microphysical property tests were designed in order to reveal the reasons for the special permeability of coral sand from the microcosmic point of view. The conversion equation of the hydraulic conductivity between quartz sand and coral sand was established. Finally, through numerical simulation, the variation rule and the parameter sensitivity of a freshwater lens were studied when the hydraulic conductivity changed within the reasonable range of natural existence. It was found that the special permeability of coral sand was caused by four factors, including roundness (Φ), roughness (Ψ), surface charge, and the surface hydrophilicity of the particles. Among the four factors, the main factors and the secondary factors were classified according to the influencing degree that changed with the sizes of the particles. The influencing sensitivity of the hydraulic conductivity on the properties of the freshwater lens had the following order: freshwater appearance time > steady-state freshwater reserves > thickness of the steady-state freshwater lens> lens stabilization time.