This study focuses on developing a biodegradable film using a novel hybrid citrus peel pectin. A bilayer approach with PLA was proposed and optimized using Response Surface Methodology (RSM) to complement pectin films’ mechanical and barrier property limitations. The optimized film composition (2.90 g PLA and 1.96 g pectin) showed enhanced mechanical strength with a tensile strength (TS) of 7.04 MPa and an elongation at break (EAB) of 462.63%. In addition, it demonstrated lower water vapor (1.45 × 10−10 g/msPa), oxygen (2.79 × 10−7 g/ms) permeability, and solubility (23.53%). Compared to single-layer pectin films, the optimized bilayer film had a 25% increased thickness, significantly improved water barrier (3806 times lower) and oxygen barrier (3.68 times lower) properties, and 22.38 times higher stretchability, attributed to hydrogen bond formation, as confirmed by FTIR analysis. The bilayer film, effectively protected against UV and visible light, could be a barrier against light-induced lipid oxidation. Moreover, it demonstrated superior seal efficiency, ensuring secure sealing in practical applications. The bilayer pouch containing mustard dressing exhibited stable sealing with no leakage after immersion in hot water and ethanol, making it suitable for secure food pouch packaging.