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Per- and polyfluoroalkyl substances (PFASs) have recently garnered considerable concerns regarding their impacts on human and ecological health. Despite the important roles of polyamide membranes in remediating PFASs contaminated water, the governing factors influencing PFAS transport across these membranes remain elusive. In this study, we investigate PFAS rejection by polyamide membranes using two machine learning (ML) models, namely XGBoost and multimodal transformer models. Utilizing the Shapley additive explanation method for XGBoost model interpretation unveils the impacts of both PFAS characteristics and membrane properties on model predictions. The examination of the impacts of chemical structure involves interpreting the multimodal transformer model incorporated with simplified molecular input line entry system strings through heatmaps, providing a visual representation of the attention score assigned to each atom of PFAS molecules. Both ML interpretation methods highlight the dominance of electrostatic interaction in governing PFAS transport across polyamide membranes. The roles of functional groups in altering PFAS transport across membranes are further revealed by molecular simulations. The combination of ML with computer simulations not only advances our knowledge of PFAS removal by polyamide membranes, but also provides an innovative approach to facilitate data-driven feature selection for the development of high-performance membranes with improved PFAS removal efficiency.