The solute-membrane interactions play an important role in adsorption and consequently rejection of trace organic compounds (TrOCs) by nanofiltration (NF) membranes, while the various specific interactions are yet to be identified and quantified. In this study, molecular docking was for the first time explored as a simulation and computation approach to elucidating the solute-membrane interactions. The binding modes between several pharmaceuticals (PhACs) and the polyamide (PA) material in different protonation/deprotonation states were simulated, and the specific interactions including hydrogen bonding, pi-pi stacking, pi-cation interaction and ionic bridge binding were identified. Binding energies consisting of van der Waals and electrostatic components were calculated by the Grid scoring of docking, which quantitatively confirmed the contributions of various interactions to the adsorption of PhACs onto the membrane. Regression analysis showed that the adsorbed amounts could be well described jointly by the binding energies and two molecular descriptors of PhACs (i.e., solubility (logS) and polarity (MR)), which depict the effects of solute-membrane and solute-water interactions, respectively. This study provided valuable information to better understanding the adsorption mechanisms which greatly affect the rejection of TrOCs by NF membranes.