To optimize the extracting procedure of polysaccharides from Indigowood Root( Isatisindigotica Fort.)and protein removal conditions. The Box-Behnken design was used to investigate the effects of processing parameters of extraction from Indigowood Root onthe yield of polysaccharides. Three independent variables such as solid to solvent radio,extraction temperature and extraction time were studied. The optimal conditions were determined and three-dimensional response surfaces wereplotted from the mathematical models. Considering the efficiency,the optimum conditions of polysaccharides extraction were solid to solvent radio of 1∶ 55,extraction temperature of 80℃,and extraction time of 3. 5 h. Under optimized conditions,the experimental yield of 3. 55% agreed closely with the predicted yield.Furthermore,four methods of Sevag,TCA,pepsin and trypsin for removing protein in crude polysaccharides extracted from Indigowood Root were evaluatedand compared based on deproteination efficiency and polysaccharide loss. The results indicated that the pepsin and trypsin methods were better than the othertwo methodswith protein removal rate of63. 5% and 52. 9% respectively,and with less polysaccharide loss. Theenzymic methods were simple,pollution-freeand suitable to remove protein in crude polysaccharides from Indigowood Root.