Membrane technology has been prevalently employed to treat high-saline organic wastewater, yet the ongoing hurdle of membrane fouling impedes the advancement and widespread implementation of membrane processes. To date, limited works had been devoted to comprehending the mechanisms of fouling development influenced by high salinity, particularly from the perspective of intermolecular interactions at a deeper level. This work filled the knowledge gap by deciphering the mechanisms underlying humic acid (HA) fouling formation under high salinity mainly using molecular dynamics (MD) simulations, which overcome the spatial scale limitation of traditional experiments and provide new mechanistic insights from the molecular level. The MD results demonstrated that Na+ primarily coordinated and bonded with the carboxyl oxygen and hydroxyl oxygen of HA through Na–O bonds, which reduced the surface charge of HA and solubility in water. Subsequently, HA swiftly migrated and deposited on membrane surface, with the molecular configuration dramatically changed from coiled state to elongated state observed under high salinity. Compared to the scenario without salt, the distribution of HA was found to be more concentrated and closer to the membrane surface, and the position of the lowest free energy decreased significantly from 0.88 nm to 0.5 nm, reflective of complete adsorption occurred. The results of real fouling experiments verified the enhanced fouling formation indeed occurred induced by high salinity, where notable NaCl crystallization appeared on the fouling layer, potentially heightening the porosity and roughness of fouling layer. This work proposed the in-depth HA fouling mechanisms under high-saline conditions from the intermolecular interaction perspective, which should offer theoretical guidance for fouling control when treating high-saline organic wastewater using membrane-based techniques.