Coral sand is an important composition of tropical islands topsoil, and it is the premise of correctly understanding and evaluating the groundwater quality of islands to carry out the hydrochemical study of atmospheric precipitation infiltrated through sand layer. In this study, the surface sand soil layers (No. D1, D2 and D3) from three different plots of tropical islands in China were collected in August 2017. Based on the simulated rainfall experiment, the characteristics of the basic physiochemical parameters of water infiltration were analyzed. At the same time, the characteristics of hydrochemical change and main controlling process infiltrated through different sand soil layers were revealed by using hydrochemical phase diagram, visual MINTEQ hydrogeochemical simulation, indices of base exchange (IBE) calculation and Gibbs diagram. The results showed that the degree of salinization of coral sands was high. The ranges of pH values of water samples through D1, D2 and D3 were 7.92-8.81, 7.86-9.30 and 7.82-9.35, respectively, which were obviously higher than the mean value of atmospheric precipitation (6.0), and EC decreased from 48.50, 89.90 and 77.60 mS/cm to 131.4, 111.6 and 98.4 μS/cm, respectively. The concentrations of many trace elements in the water infiltrated through D1, D2 and D3 gradually decreased with rainfall washing. Among them, Al, As, B (D1 and D2) and Cr, Fe, Pb were more difficult to be dissolved in water, which should be paid more attention. The concentrations of main ions in water stored at D1, D2 and D3 were Na⁺>Mg²⁺>Ca²⁺>K⁺ and Cl^->SO₄^2->HCO₃^->NO₃^-> CO₃^2->Br^->F^-, and their chemical types of water were changed from Cl-Na to HCO₃-Na·Ca·Mg water with rainfall elution. The controlling mechanisms of the hydrochemistry penetrating the coral sand layer included the dissolution and precipitation of carbonate, chloride and sulfate minerals, and the exchange of between (Na⁺, K⁺) and (Ca⁺, Mg⁺) ions during precipitation infiltration. This study is of great scientific significance to guide the rational development and utilization of groundwater resources, to ensure the safety of water of residents and to maintain the ecosystem in the tropical island.