To elucidate the regulatory effect of linoleic acid (LA) on the interaction between β-conglycinin (7S) and glycinin (11S) and the physicochemical properties of their composite films, the interactions of LA with the 7S-11S complex and glycerol were investigated using molecular dynamics (MD) simulation, and the effect of LA on the performance of 7S-11S composite films was examine. MD simulation demonstrated that the radius of gyration, solvent-accessible surface area, and hydrophobic surface area of the 7S-11S complex increased with increasing LA content, while intermolecular interactions weakened, with the total binding free energy increasing from -114.31 to -1.61 kcal/mol. Meanwhile, hydrogen bonds and van der Waals forces between LA and the complex as well as those between LA and glycerol strengthened with increasing LA content. The addition of LA reduced the tensile strength and water vapor permeability of 7S-11S composite films but enhanced the elongation at break and surface water contact angle. Fourier transform infrared spectroscopy (FTIR) analysis indicated that LA weakened the O-H stretching vibration peak while intensifying the C-H stretching vibrations at 3011, 2926, and 2855 cm^-1. Moreover, the proportion of hydrophobic interactions in the 7S-11S composite films increased with LA content, leading to the formation of insoluble aggregates of high-molecular-mass components involved in hydrogen bonding and hydrophobic interactions. This study has elucidated that LA modulates protein-based film extensibility and hydrophobicity by regulating 7S-11S interactions and intermolecular forces, providing theoretical insights for developing soy protein-based edible films.