To address the environmental issues caused by the poor degradability of petrochemical-based cling films, efforts are being made to develop a biodegradable composite film with enhanced barrier and antibacterial properties for fruit and vegetable preservation. Soy protein isolate (SPI) and chitosan (CS) were used as the matrix materials, while amphiphilic esterified lignosulfonate (ELS) was synthesized via a deep eutectic solvent (DES) method and introduced as a compatibilizer into the SPI-CS system. The resulting SPI-CS-ELS composite films were fabricated through solution casting. The results revealed that ELS acted as a molecular bridge, forming stable interactions with SPI and CS through electrostatic attraction, hydrophobic interactions and hydrogen bonding, thereby constructing a homogeneous and compact three-dimensional network structure. Compared with SPI and SPI-CS films, the SPI-CS-ELS composite films exhibited significantly improved mechanical strength, superior water vapor and oxygen barrier properties. Moreover, the inhibition rates against Escherichia coli and Staphylococcus aureus exceeded 99%. The SPI-CS-ELS composite film provides a new strategy for developing high-performance biodegradable food packaging materials.