The invention discloses a flocculating agent for an impurity removal process of steviol glycosides. The flocculating agent comprises, by weight, 10-20 parts of modified chitosan, 15-25 parts of modified lignin, 30-40 parts of polymeric ferric sulfate, 25-35 parts of aluminium citrate, 10-15 parts of magnesium sulfate, 20-30 parts of polymeric ferric silicate-sulfate, 3-5 parts of porous pearlite powder and 4-6 parts of zeolite powder. A preparation method of the modified chitosan comprises the steps that carboxymethyl chitosan is added into a sodium hydroxide aqueous solution, after heating and heat preservation are conducted, a 3-chloro-2-hydroxypropyltrimethylammonium chloride aqueous solution is dropwise added, the heat preservation is continuously conducted, and then the mixture is adjusted to be neutral to obtain a first material; the first first material is added into ethyl alcohol, filtration is conducted, and a second material is obtained after drying; the second material is added into distilled water to be evenly stirred, water-bath heating is conducted, acrylamide and an initiating agent are sequentially and dropwise added, and a third material is obtained after the heat preservation is conducted; the third material is added into acetone, the filtration is conducted, and the modified chitosan is obtained after drying is conducted.