Abstract: Sea water intrusion is an important environmental issue that plagues the economic and social development in coastal areas. The implementation of quantitative simulation, prediction and visual management of sea water intrusion is a cost-effective means for monitoring and mechanism analysis of sea water intrusion, which can provide important theoretical and technical supports for the formulation of sea water intrusion control measures. VFT3D was proposed to model the sea water intrusion processes and predict the impacts on groundwater, which can comprehensively consider the effects of surface water and groundwater, simulate variable-density groundwater flow, and solve complex reactive migration problems. This article provides an introduction to the VFT3D model and presents an application of VFT3D to modeling seawater intrusion process. The simulated results are compared with those of the SEAWAT. The results show that the simulated water heads with VFT3D are close to the SEAWAT simulation results. The SEAWAT is unable to simulate complex chemical reactions during the sea water intrusion. The results indicate that geochemical processes (cation adsorption and exchange) have a significant effect on the movement of cations (Na⁺, K⁺, Mg²⁺ and Ca²⁺). Geochemical process leads to the concentration change in the transition zone, whose influence on the process of sea water intrusion can not be ignored. Therefore, the variable density and complex reaction process should be involved to more accurately describe the sea water intrusion, which can benefit the implementation of the underground saltwater remediation and management.