Sodium alginate (SA)-pectin (PEC)-whey protein isolate (WPI) complexes were used as an emulsifier to prepare β-carotene emulsions, and the encapsulation efficiency for β-carotene was up to 93.08%. The confocal laser scanning microscope (CLSM) and scanning electron microscope (SEM) images showed that the SA-PEC-WPI emulsion had a compact network structure. The SA-PEC-WPI emulsion exhibited shear-thinning behavior and was in a semi-dilute or weak network state. The SA-PEC-WPI stabilized β-carotene emulsion had better thermal, physical and chemical stability. A small amount of β-carotene (19.46 ± 1.33%) was released from SA-PEC-WPI stabilized β-carotene emulsion in simulated gastric digestion, while a large amount of β-carotene (90.33 ± 1.58%) was released in simulated intestinal digestion. Fourier transform infrared (FTIR) experiments indicated that the formation of SA-PEC-WPI stabilized β-carotene emulsion was attributed to the electrostatic and hydrogen bonding interactions between WPI and SA or PEC, and the hydrophobic interactions between β-carotene and WPI. These results can facilitate the design of polysaccharide-protein stabilized emulsions with high encapsulation efficiency and stability for nutraceutical delivery in food and supplement products.