Sustainable bio-based active films are promising alternative materials that can alleviate the growing environmental problems. Apple processing generates a large number of by-products rich in pectin and polyphenols. Herein, we extracted apple pectin (Apec) from apple pomace, developed a multifunctional bilayer film based on Apec and chitosan by incorporating inclusion complex of apple polyphenol and hydroxypropyl-β-cyclodextrin (ICAH). The results showed that the incorporation of ICAH remarkably improved the mechanical strength, barrier properties, and the thermal stability of the films. Meanwhile, the composite films loaded with ICAH exhibited potent antioxidant and antibacterial activities in vitro. Furthermore, a 7-day shelf-life analysis on fresh pork verified that the films were effective in maintaining the pH level (below 6.0), reducing the thiobarbituric acid reactive substance (from 1.18 to 0.63 mg MDA/kg) and total volatile basic nitrogen (from 23.27 to 14.03 mg/100 g), and inhibiting the microbial growth (from 6.83 to 3.74 log CFU/g), thereby obtaining a satisfactory sensory evaluation. The pork wrapped with the films can significantly extend the period of freshness from 4 days to 7 days under refrigeration at 4 °C. The results suggest that the prepared composite films hold promise as an active packaging material for application in pork preservation.