Abstract: Per- and polyfluoroalkyl substances (PFAS) are a class of ubiquitous and persistent pollutants that pose significant risks to drinking water and human health. Considerable progress has been made in understanding the transport processes of PFAS in soil over the past decade; however, there is a lack of quantitative studies on the migration and transformation of PFAS in groundwater under complex hydrodynamic conditions. This study, focusing on perfluorohexane sulfonate (PFHxS), investigated the migration and transformation mechanisms of PFAS under variably saturated flow conditions. The influence of stratum heterogeneity and water table fluctuations on the migration and transformation of PFHxS in groundwater was explored. By simulating the migration and transformation processes of PFHxS in the aqueous phase, solid phase, and air-water interface, the migration and transformation behavior patterns of PFHxS under surface water-groundwater interaction condition in riparian zone was investigated. The results show that high permeability areas of heterogeneous layers create preferential channels for flow and transport, accelerating the migration of PFHxS to riparian zones The interaction between surface water and groundwater caused by rainfall led to the spatial redistribution of PFHxS pollution plume and extended the coverage of PFHxS pollution area. The presence of preferential flow accelerates the response rate of PFHxS in the surface water-groundwater interaction. This study contributes to enhancing the accuracy of predicting the extent of pollution spread in similar complex environments, optimizing monitoring and response measures, and providing a scientific basis for pollution emergency management.