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Pectin, a complex hydrocolloid, attracts extensive attention and application stemming from its good emulsification. However, the source of emulsification remains a conundrum. In this experiment, the structures of six kinds of commercial pectin, including LM 101 AS (101), LM 104 AS (104), 121 SLOW SET (121), YM 150 H (150), LM 13 CG (13CG), and β-PECTIN (β-P) were determined, and the effects of pectin structure on emulsion emulsification, rheology and in vitro digestibility were studied. The results showed that the β-P pectin contained a higher content of protein, ferulic acid, and acetyl and had a lower interfacial tension; this pectin-stabilized emulsion exhibited a smaller droplet size and superior centrifugal and storage stability. The results showed that β-P pectin had higher contents of protein, ferulic acid, and acetyl and lower interfacial tension than other pectins, and its stabilized emulsion exhibited smaller droplet size and superior centrifugation and storage stability. Furthermore, the emulsion formed by the pectin with high molecular weight and degree of methoxylation (DM) had a higher viscosity, which can inhibit the aggregation of emulsion droplets to some extent. However, the DM of pectin affected the charge and digestion behavior of pectin emulsion to a great extent. The smaller the DM, the more negative charge the emulsion carried, and the higher the release rate of free fatty acids. The results provided a basis for the rational selection and structural design of the pectin emulsifier.