Abstract: Pneumococcal vaccine plays a key role in preventing diseases such as pneumonia and meningitis caused by Streptococcus pneumoniae (S. pneumoniae). Capsular polysaccharide, C-polysaccharide and phosphorus content are important indicators for quality control of polysaccharide antigens in vaccine development and production. In this study, a quantitative 1H NMR and 31P NMR method based on a single internal standard hexamethylphosphoramide (HMPA) was developed to achieve simultaneous determination of capsular polysaccharide, C-polysaccharide and phosphorus content in 6A, 6B, 18C, 19A, 19F and 23F S. pneumoniae polysaccharide antigens. Using the internal reference comparison method, the effect of solubility of polysaccharide on quantitative 1H NMR determination was investigated. It was found that the determination results of quantitative 1H NMR were affected by the viscosity and concentration of polysaccharide solution. It was found that high viscosity polysaccharides at 3−15 mg/mL and low viscosity polysaccharides at 5−25 mg/mL were the optimal detection solution concentration range. This “one internal standard three quantitative” NMR method has good precision, specificity and accuracy, and provides a valuable new strategy for the quality control of pneumococcal vaccine.