Developing environmentally sustainable biodegradable multifunctional bio-composite films is an effective strategy for ensuring food chain security. This study initially prepared inclusion complexes (HP-(3-CD@EGCG) of Hydroxypropyl-(3-cyclodextrin (HP-(3-CD) and EGCG to ameliorate the stability of EGCG. Then HP-(3-CD@EGCG and different ratios of lignin were incorporated into gelatin solution through cross-linking polymerization to prepare an antioxidant, antibacterial and biodegradable composite film (HP-(3-CD@EGCG/Lignin/Gelatin). The results illustrated that HP-(3-CD crosslinked with EGCG and the encapsulation rate of EGCG reached 82.26%, and lignin increased the comprehensive characteristics of the gelatin-based composite films. The hydrophobicity of the composite films increased with increasing lignin concentration, reaching a water contact angle of 117.33 degrees; Furthermore, the mechanical characteristics and UV-light/water/oxygen barrier capacity also increased significantly. The composite films showed excellent antioxidant and antimicrobial properties, which also verified in the preservation of tomatoes and oranges, extending the shelf life of the fruit. It is worth mentioning that lignin has no effect on the biodegradability of the composite film, and the degradation rate in the soil reached 80% on the 10th day. In summary, biodegradable multifunctional environmentally friendly composite films based on gelatin and loaded with lignin and HP-(3-CD@EGCG inclusion complexes are anticipated to be applied in fruit and vegetable preservation.