Although nanofiltration (NF) has been widely reported for removing long-chain per- and polyfluoroalkyl substances (PFAS) from water, little is known about the correlations between removal efficacy and PFAS/membrane characteristics, especially for emerging PFAS with shorter polyfluoroalkyl chain or containing fluoroether moieties. A systematic study of treatment of structurally diverse PFAS by NF can help predict the behavior of more unknown compounds during NF process. In this study, we conducted filtration experiments with five commercial NF membranes. Results show that seven legacy PFAS, three emerging perfluoroalkyl ether acids (PFEA) and two fluorotelomer sulfonates (FTS) can be removed simultaneously during the NF process, with rejection ranging from 66.0% to > 99.9%. The removal efficiency of five membranes decreased successively as DK > NF90 > XN45 > NF270 > DL. Rejection of FTS and PFEA by DK membranes were 88.3% to 97.1% and 81.7% to > 99.9%, respectively. Correlation analysis revealed that PFAS molecular structure and membrane characteristics significantly affect PFAS rejection. PFAS molecular weight (MW) and hydrophobicity (logKow) and membrane intrinsic structural characteristics (e.g., molecular weight cut-off (MWCO), water permeability, and salt selectivity) are among the most significant parameters impacting PFAS removal. The findings imply that both steric hindrance and hydrophobic interactions contribute to PFAS rejection. Moreover, the mass of PFAS adsorbed on the membrane was positively correlated with their molecular parameters (i.e., MW and logKow) and weakly correlated with membrane properties, suggesting that the adsorption and rejection of PFAS have similar driving forces. This study provides critical insights into the application of NF for emerging PFAS removal for both the scientific community and private industry, concerning water purification processes and remediation of thousands of PFAS-impacted sites.