The chemical modification is important to improve the solubility to various solvents, physical properties, and immunological functions in polysaccharide chemistry. Oxidation is one of the familiar methods in the chemical modification of polysaccharides not only for industrial applications but also in fundamental studies, such as the structural determination, the first step of the functionalization, and so on. We focus a triple helical polysaccharide, schizophyllan, to study the effects of the carboxylation on the ordered structure of the polysaccharide. The oxidation of schizophyllan side chains is performed by two-step oxidation using periodate and chlorite in aqueous solutions to obtain the carboxylated sample, showing the polyelectrolyte character. The carboxylation of schizophyllan affects the triple helical conformation and the order-disorder transition with respect to the schizophyllan side chain in aqueous solutions, and solution properties governed by the conformation of this polysaccharide. The triple helical conformation was investigated mainly using the size-exclusion chromatography with a multi-angle light scattering detector, and the order-disorder transition with respect to the schizophyllan side chain was studied by differential scanning calorimetry and optical rotation.