Abstract: To enhance the economic value of flaxseed processing by-products while addressing the challenges of astaxanthin's poor water solubility, low stability, and limited bioavailability, this study developed composite emulsifiers (FP/PCs) via electrostatic interactions between flaxseed meal protein (FP) and pectin (PC) to stabilize astaxanthin-loaded emulsions. The potential therapeutic application of these emulsions in non-alcoholic fatty liver disease (NAFLD) was further investigated. The optimal pH for FP/PC complex formation was determined to be 3.5 based on Zeta potential measurements. Wettability analysis revealed that FP/PC-1.00% exhibited the highest three-phase contact angle (74.2°). In vitro simulated digestion and antioxidant assays were conducted to evaluate the emulsion's protective effects on astaxanthin and its functional bioactivity. Notably, F-1.00%-AXT retained 66.98% of astaxanthin after digestion, with the resulting emulsion micelles (FM-AXT) displaying a particle size of 507 nm—suitable for cellular uptake. In an oleic acid-induced NAFLD cell model, FX-AXT outperformed free astaxanthin by significantly reducing intracellular ROS levels (P<0.01), demonstrating enhanced antioxidant capacity. Furthermore, Oil Red O staining and quantitative lipid analysis (TG, T-CHO) confirmed FX-AXT's potent lipid-lowering effects. This study successfully engineered a flaxseed by-product-derived protein/pectin composite emulsion that improved astaxanthin delivery and bioactivity. The findings present a promising functional food-based strategy for NAFLD management while adding value to flaxseed processing waste.