Due to the complex composition and structure of plant polymers, a detailed investigation into the emulsification mechanism of pectin is still warranted. Herein, we aimed to clarify the relationship between the macromolecular structure (conformational flexibility and molecular weight (M_w) and the emulsification performance of pectin, which was obtained from two sources (sugar beet pectin (SBP) and citrus pectin (CP) and treated by hydrothermal depolymerization (dominated by acid hydrolysis), following which the overall flexibility was assessed using the persistence length (L_p)/M_w per unit contour length (M_L) ratio. The results showed that depolymerization reduced the conformational flexibility of SBP (L_p/M_L increased from 0.0169 to 0.0219 nm² mol/g) and improved the flexibility of CP (L_p/M_L decreased from 0.0551 to 0.0403 nm² mol/g). Interfacial tension analysis revealed that the higher flexibility of pectin conferred superior surface activity, leading to decreased interfacial tension. Consequently, the fabricated emulsion was finer and more stable, with smaller changes in droplet size, as measured by a laser particle analyzer. The improved emulsification was attributed to the better exposure of hydrophobic proteins due to the conformational changes caused by the stretching and twisting of the more flexible polysaccharide chains in pectin, which facilitated higher interfacial adsorption of CP, increasing it from 43.4% to 61.8%. Moreover, the smaller interfacial concentration of the flexible pectins suggested that they had higher emulsification efficiency, in which the pectins might be densely packed at the interface to form a compact interfacial layer to stabilize the emulsion.