Post-harvest spoilage of strawberries is a pressing issue that requires urgent attention. This study successfully isolated and identified two saprophytic fungi responsible for strawberry rot-Aspergillus tubingensis and Alternaria alternata. Subsequently, the response surface methodology was employed to optimize the concentration ratios of citral, geraniol, and menthol, aiming to maximize their combined effect on inhibiting fungal growth. Molecular docking techniques were employed to investigate the binding targets of these active substances with 14α-demethylase (CYP51). The antifungal agents at optimized concentrations were loaded into γ-cyclodextrin metal-organic frameworks (γ-CD-MOFs) and uniformly dispersed within a multilayer film composed of phenolic acid-grafted modified chitosan. This approach significantly enhanced (P < 0.05) the mechanical properties of chitosan, including fracture tensile strain among others, while also endowed it with dual functionalities of antifungal and antioxidant effects. Additionally, it offered excellent controlled-release characteristics, ensuring a steady and continuous release of active ingredients. Finally, the application of multilayer films to postharvest strawberries significantly reduced the decay rate (P < 0.001) and weight loss (P < 0.05), while also limiting their respiratory intensity. In summary, the multilayer film demonstrates excellent preservation effects on strawberries, thus holding broad application prospects in food preservation.