Deproteinization procedure is a fundamental step for analyzing polysaccharide from natural plants. In this study, in the course of refining bioactive polysaccharides from lingzhi (Ganoderma atrum), an effective deproteinization method using lead acetate solution was established by comparing with other available methods. The percentages of deproteinization, polysaccharide loss, and its antioxidant activities loss were used as the index to evaluate and optimize the precipitation experimental conditions. The results showed that the modified method, precipitation with the addition of 0.4-0.52%(w/v) lead acetate, was superior to the others, as evidenced by the highest deproteinization efficiency (88%), as well as the lowest polysaccharide loss (17%). And notably its antioxidant activity also remained good (loss 15%). It provides a simple prefractionation step for the analysis of polysaccharide from natural plants. Polysaccharide isolated by this method is in the native state. Our method may offer a rapid method for removing protein from plant polysaccharides in large scale.