Abstract: Soil-groundwater coupled numerical simulation is the main method to quantitatively describe the flow and solute transport in a groundwater system. The existing researches on a large-scale site are limited by the difficulty of data acquisition and the amount of simulation calculation. Most of them divide the soil and groundwater into two systems, and it is of great significance to study the soil and groundwater as a whole system. In order to accurately depict the migration of contaminants in the soil-groundwater system of the actual site and reveal the parameter sensitivity of the variable saturation reaction solute transport model, in this paper, a 3D soil-groundwater model is established by using the Galerkin finite element method to quantitatively describe the migration of hexavalent chromium in soil-groundwater based on the data obtained from field tests and previous studies. The fluctuation of phreatic surface in the soil-groundwater system is studied by changing the recharge conditions. The effects of retardation coefficient and reaction constant on solute transport are discussed. The results show that in the soil, the maximum horizontal migration distance of contaminants is 300 m to the southeast of the site; the maximum distribution area of contamination halo in groundwater is about 1.632 km²; the vertical hexavalent chromium in soil only needs 15.6 h to infiltrate into the phreatic surface, and penetrates through the aquifer in the sixth day. When the groundwater level fluctuates with the change of recharge, hexavalent chromium in groundwater will enter the soil with the water flow, affecting the distribution of contamination in the soil. The discussion of solute transport parameters shows that when the reaction constant increases from 0 to 10^-6s^-1, the concentration of the contaminants in groundwater decreases by about 2000 mg/L at the boundary of the migration site, which makes it difficult to migrate to the Lianshui River. The numerical model based on FEFLOW can solve the problem of poor interaction between systems and provide more accurate simulation results.