The invention discloses a preparation method of a starch-based composite flocculant. The preparation method comprises: dissolving starch in water to obtain a 10-20% starch solution, slowly adding NaOH to the 50-60 DEG C water bath at a uniform speed according to a mass ratio of the NaOH to the starch of 1:8-12, and carrying out a stirring reaction for 40-80 min to obtain a modified starch solution; adjusting the pH value of the modified starch solution to 2.0-3.5 with sulfuric acid; and adding polysilicate ferric to the modified starch solution according to a ratio of the starch to the polysilicate ferric of 0.25-0.5:1, maintaining the pH value at 2.0-3.0, carrying out a reaction for 3.5-4.5 h in a 50-60 DEG C constant temperature oscillator, and standing overnight so as to age. According to the present invention, the starch-based composite flocculant has characteristics of no toxicity and no residue, has the SS removal efficiency of more than 90%, and has the COD removal efficiency of more than 60%, wherein the treatment cost is 0.2 yuan/m<3>, and the separated pig manure can further be directly used as the fertilizer for fruit trees and forest, and can be used as the raw material of the organic fertilizer.