This study investigated the effects of varying concentrations of peanut shell flavonoids (PSFs) on the properties of peanut meal extract‐tilapia skin protein composite films and their impact on cherry tomatoes preservation. Peanut meal alcohol extract (Pe) and tilapia skin protein (Co) were used as base materials, combined with PSFs to prepare composite films with excellent antioxidant properties. The results demonstrated that the optimized composite films exhibited superior mechanical properties, with a tensile strength of 9.83 MPa and an elongation at break of 204.04%. Increased flavonoid content enhanced the films' antioxidant capacity, achieving superoxide anion and DPPH radical scavenging rates of 15.08% and 21.37%, respectively. The microstructure, IR spectra, and circular dichroism spectra of the composite films are also significantly different with the change of flavonoid content. In the cherry tomato preservation experiment, the PeCo‐0.5 composite film treatment group maintained a low weight loss rate (11.18%) and malondialdehyde content (13.33 μmol/g) after 15 days, delayed the peak respiration rate, and significantly reduced the peak respiration intensity (3.43 mgCO2∙ mg−1∙gh−1). At the same time, the activity of polyphenol oxidase in the tissue of Cherry Tomatoes was significantly inhibited, and the decrease rate of Vc content was also significantly decreased, which effectively preserving the bright color, smooth appearance, and good aroma of the cherry tomatoes. This study not only provides new insights into the comprehensive utilization of tilapia skin and peanut by‐products but also opens new avenues for the development and application of fruit and vegetable preservation films.