The physicochemical properties and applications of polysaccharides are highly dependent on their chemical structures, including the monosaccharide composition, degree of substitution, and position of substituent groups in the backbone. The occurrence of side groups or side chains in the chain backbone of polysaccharides is often an essential factor influencing their conformational and physicochemical properties. Welan gum produced by the fermentation of Sphingomonas sp. ATCC 31555 microorganisms has been widely used in food, construction, and oil drilling fields. While understanding the physicochemical properties of welan gum solution has been highly developed, there is still little information about the determination strategy of the glycosyl side groups in welan gum. In this study, the NMR method was established to quantitatively determine the substituent groups in the chain backbone of welan gum. The delicate chemical structures of welan gum obtained at different fermentation conditions were clarified. The composition and content of side substituents were also identified by high-performance liquid chromatography to confirm the accuracy of NMR analysis. The quantitative determination of substituent groups in gellan gum based on NMR analysis was also elaborated for comparison. This work provides insights for profoundly understanding the structure-function relationship of welan gum.