The purification process of Folium Isatidis polysaccharide (FIP) was optimized by response surface method (RSM) using AB-8 macroporous resin. A major homogeneous polysaccharide, named FIP-II, was purified from FIP through DEAE-650 M and Sephadex G-75 column chromatography. The structure of the FIP-II was investigated through the combination of HPLC, GC, FT-IR, sequential acid hydrolysis, peroxide oxidation, Smith degradation, and NMR analysis. Then, the sulfated, phosphorylated, and carboxymethylated derivatives of FIP-II, namely FIPII-S, FIP-II-P, and FIP-II-C, were prepared. Their structures were characterized by extensive analysis of chromatographic and spectroscopic methods including UV, HPLC, GC, FT-IR, Congo red, CD, SEM-EDX, XRD, TG, DTG, and DSC. Results of RSM showed that optimum purification conditions were elution flow rate 2.76 BV/ h, the sample concentration 2.03 mg/mL, and the elution volume was 1.26 BV. The average comprehensive score of purification was up to 76.28%. FIP-II and its derivatives were heteropolysaccharides composed of different molar ratios of rhamnose, arabinose, xylose, mannose, glucose, and galactose, with a molecular weight of 775.64, 911.75, 1288.31, and 1013.61 kDa. The structure modification influences the solution conformation, surface morphology, crystalline nature, and thermal properties of the FIP-II and its derivatives. Antioxidant activity tests showed that structure modification could significantly enhance the activity of the polysaccharides differently. It could be a potential ingredient in the functional food and pharmaceutical industry.