In the current study, water soluble yellow mustard mucilage (WSM) was used as a model to study the conformation-emulsification property relationship of polysaccharides. Native WSM molecules were exposed to pectinase to hydrolyze, and the depolymerized fractions were collected from 0 to 6 h. The molecular weight (Mw) distribution of the collected fractions ranged from 1.60 to 2.33 × 106 Da, while their conformational parameters, namely radius of gyration (Rg), hydrodynamic radius (Rh) and ρ value (Rg/Rh), varied significantly (P < 0.05). Surface tension, flow behavior, droplet size, zeta-potential, solubility, emulsion creaming stability, and freeze-thaw stability of the depolymerized fractions were compared with the native WSM. The results indicated that depolymerized fractions showed no difference in surface tension, solubility and flow behavior compared to the native WSM. The fractions obtained at 2, 3 and 4 h of pectinase hydrolysis exhibited the most rigid conformation, and their corresponding emulsions possessed the smallest droplet size with the highest zeta-potential value. The native WSM and the fractions obtained from 0.5 to 6 h of pectinase hydrolysis exhibited the most flexible conformation, and showed the best emulsion creaming stability and freeze-thaw stability after going through 3 freeze-thaw cycles. It is concluded that a flexible conformation may lead to a more stable emulsion at a similar molecular weight range. The results may provide useful insight to food industries for applications of WSM and its hydrolyzed fractions as novel ingredients.