Objective To explore the stability of type 6A pneumococcal capsular polysaccharide (Pn6A) with different chain lengths and effect of chain length on the stability and immunogenicity of conjugates. Methods Pn6As with different chain lengths were obtained by high pressure homogenizer, then activated by 1-cyano-4-dimethylaminopyridinium tetrafluoroborate to form conjugates with tetanus toxoid-adipic acid dihydrazide derivatives. The structure was verified by proton nuclear magnetic resonance spectroscopy (1H-NMR) comparison of the original polysaccharides, polysaccharides degradation products and conjugates, and the antigenicity was quantitatively compared by anthrone sulfate method and the rate nephelometry method. The stability of polysaccharides with different chain lengths was compared by high performance liquid-size exclusion chromatography-multiangle laser scatter. The physical chemistry properties of conjugates were analyzed, and the stability of conjugates was compared by changes in the weight-average relative molecular weight (Mw) and free polysaccharides. NIH mice were immunized subcutaneously with original polysaccharides and conjugates for 3 doses, respectively, and the IgG levels were determined by ELISA. Results The Mw of polysaccharides sheared 3, 8, 20 times decreased from 14.01×105 g/mol to 1.55×105, 0.92×105 and 0.58×105 g/mol, respectively, and the corresponding conjugates physical chemistry data were similar. The 1H-NMR results showed that the chemical shift of each characteristic proton of polysaccharides degradation products and conjugates did not change from original polysaccharides. The unit antigen values of the polysaccharides and conjugates were similar. The changes of Mw and free polysaccharides of the long chain polysaccharides and conjugates were greater than those of short chain polysaccharides and conjugates under different pH and temperature conditions. The IgG levels of mice immunized with conjugates with different chain lengths were statistically significantly higher than that with original polysaccharide (F=2.90,P=0.048), but there was no statistically significant difference in immunogenicity among the different conjugates (F=1.39,P=0.267). Conclusions Mechanical shearing does not destroy the chemical structure and antigenicity of Pn6A. The shorter the Pn6A chain lengths are, the more stable the polysaccharide and conjugates are. The conjugates from Pn6A prepared by mechanical shear show good immune response in mice.