Chitosan-based films are confronted with several technical challenges that impede their broad application in the preservation of perishable foods, such as suboptimal mechanical properties and insufficient antioxidant activity. In this work, we have introduced lignin (LG) and natural clinoptilolite zeolite (NCZ) into pure chitosan-based films to address the above limitations. The synergistic incorporation of LG and NCZ has endowed the composite films, designated as CTSLC, with a suite of enhanced attributes, including improved thermostability, enhanced UV-shielding capability and hydrophobicity, augmented antioxidant activity, refined gas selectivity, and bolstered mechanical properties. The enhancements in the antioxidant activity, gas selectivity, and mechanical properties of CTSLC are notably pronounced, reflecting a substantial advancement in their overall performance. These attributes surpass those of both pure chitosan-based film or commercial polyethylene film. Consequently, CTSLC could keep the freshness and appearance of strawberries and mangoes at least 60 hours and 10 days, respectively. The findings suggest that CTSLC has the potential to be a promising material for the preservation of perishable foods, offering a significant advancement in the field of food packaging and preservation technology.