Chlorophylls face significant challenges in practical applications due to their low physicochemical stability. This study investigated the stability of chlorophylls within chlorophyll-protein complexes derived from Auxenochlorella pyrenoidosa and developed a novel surfactant-assisted enzymatic modification strategy to enhance chlorophyll stability. Enzymatic hydrolysis with papain in the presence of Tween 80 increased chlorophyll retention to 88.77%, compared to 78.69% without surfactant, with improved stability observed across a wide temperature range (4-80°C), maintaining chlorophyll retention between 69.41% and 85.09%, as well as under acidic conditions. Mass spectrometry identified 26 chlorophylls and their derivatives, while Tween 80 mitigated the conversion of chlorophylls into undesirable brown compounds, such as pheophytins. Peptidomics and molecular docking analysis revealed that hydrophobic and hydrogen bonding interactions between chlorophylls and specific chlorophyll-binding peptides contributed to enhanced stability. This study presents a promising approach for improving chlorophyll stability through native chlorophyll-binding proteins, particularly for applications in protein-based food matrices.