In this study, the effect of component migration and interaction with concomitant saponins on the composition and functional properties of the seed storage proteins from Camellia oleifera Abel., a typical woody oil crop in China, was investigated using proteomics and molecular docking. The results showed that the optimal parameters for alkaline extraction were solid/liquid ratio 1:10 (g/mL) and pH 8.0, which resulted in an extraction rate of 75.8%, and a saponin-to-protein ratio of 2.60. The 11S globulins were precipitated at pH 4.5 with a saponin-to-protein ratio of 0.36. Albumin accounted for 69%of the total storage proteins, and coexisted with saponin during the extraction process, thus resulting in a high saponin-to-protein ratio of 3.73. The foaming properties of albumin and globulin from C. oleifera Abel. seeds were larger than 200%, and the emulsifying activity index was 16.7 m²/g. The interaction between saponins and proteins significantly improved the emulsion stability. This study provides theoretical support for the high-value utilization of proteins from C. oleifera Abel. and the development of functional food ingredients.