The invention relates to a modified natural polymer combined flocculating agent and a using method thereof. The flocculating agent is the combination of modified natural polymer and complexing agent, wherein the modified natural polymer is prepared by carrying out phosphorylation modification, sulfonation modification or etherification modification on one or combination of two in shells of shelled animals such as shrimps, crabs and insects, cotton, straw, bagasse and starch; the complexing agent is combination of at least two in magnesium chloride, calcium chloride, sodium hydroxide, potassium hydroxide, aluminium chloride, aluminum sulfate, aluminium potassium sulfate, calcium oxide, sodium tetraborate, ferric chloride, ferrous sulfate, ferrous chloride, ferric sulfate, boric acid, hydrochloric acid and sulfuric acid. After the modified natural polymer is added, the complexing agent can be added into the natural polymer at any time within 12h according to the need of flocculation, and the flocculation reaction can be immediately finished. The invention has the advantages of controllable flocculation, rapid flocculation speed, large and firm flocculating body, low water content, safety, non-toxicity and wide temperature adaptation range.