Okra pectins (OKPs) with diverse structures obtained by different extraction protocols have been used to study the relationship between their molecular structure and emulsifying properties. A targeted modification of molecular structure offers a more rigorous method for investigating the emulsifying properties of pectins. In this study, three glycoside hydrolases, polygalacturonase (PG), galactanase (GL), and arabinanase (AR), and their combinations, were used to modify the backbone and side-chains of OKP, and the relationships between the pectin structure and emulsion characteristics were examined by multivariate analysis. Enzymatic treatment significantly changed the molecular structure of OKP, as indicated by monosaccharide composition, molecular weight, and structure analysis. GL- and AR- treatments reduced side-chains, while PG-treatment increased side-chain compositions in pectin structure. We compared the performance of hydrolyzed pectins in stabilizing emulsions containing 50% v/v oil-phase and 0.25% w/v pectin. While the emulsions were stabilized by PG (93.3% stability), the emulsion stability was reduced in GL (62.5%), PG+GL+AR (37.0%), and GL+AR (34.0%) after 15-day storage. Furthermore, microscopic observation of the droplets revealed that emulsion destabilization was caused by flocculation and coalescence. Principal component analysis confirmed that neutral sugar side-chains are key for long-term emulsion stabilization and that their structure explains the emulsifying properties of OKP. Our data provide structure-function information applicable to the tailored extraction of OKP with good emulsification performance, which can be used as a natural emulsifier.