The invention discloses a boracic polysilicic acid containing aluminum sulfate and zinc sulfate and chitosan composite flocculant which is prepared from aluminum sulfate octadecahydrate, heptahydrate,sodium metasilicate nonahydrate, borax, chitosan and sulfuric acid by hybrid reaction. The molar ratio of aluminum to silicon is 0.3-0.5, the molar ratio of zinc to silicon is 0.2-0.4, the molar ratio of boron to silicon is 0.1-0.2, and the mass ratio of the chitosan to silicon is 0.04-0.15. The invention further discloses a preparation method of the boracic polysilicic acid containing aluminum sulfate and zinc sulfate and chitosan composite flocculant. The preparation method includes the steps: first, preparing polysilicic acid solution; second, preparing boracic polysilicic acid containingaluminum sulfate flocculant solution; third, preparing chitosan solution; fourth, preparing a boracic polysilicic acid containing aluminum sulfate and zinc sulfate and chitosan composite flocculant crude product; fifth, preparing the finished boracic polysilicic acid containing aluminum sulfate and zinc sulfate and chitosan composite flocculant. The composite flocculant prepared by the preparationmethod is low in cost, stable in performance, good in storage performance, convenient to use and more environmentally friendly as flocculation and algae removal are more efficient and thorough, and fewer metal ions remain in water.