In this study, polyphenols extracted from apple waste were blended with modified nanocellulose and modified microcrystalline cellulose to produce composite films based on water chestnut starch. Thermogravimetric analysis indicated that the addition of polyphenols from apple residue could enhance the heat endurance of the water chestnut starch film. The study findings suggested that the incorporation of M-NCC led to a 24.35% boost in the tensile strength of the finished films, while that with M-MCC increased by 55.17%. The hydrophobic properties were improved due to the introduction of non-polar carbon chains and hydrophobic ester groups, resulting in respective increases in the surface contact angle of 22.66% and 24.94%. The incorporation of polyphenols from apple residue led to a 16.05% increase in the water solubility of the starch film, and the incorporation of M-NCC and M-MCC resulted in a decrease in the water solubility of the composite films by 19.04% and 30.79%, respectively. Moreover, the DPPH free radical scavenging rates of the films containing apple polyphenols (P, PN, and PM) were increased by 164.7%, 163.3%, and 134.7%, demonstrating excellent antioxidant properties. These findings suggested that the combination of apple pomace polyphenols and cellulose nanocrystals offered an optional approach for preparing food packaging films.