The invention discloses a compound chitosan flocculant for treating desulfurization waste water, and a preparation method and application thereof. The method comprises the following steps: adding chitosan into an acetic acid solution and uniformly mixing; adding ferric sulfate and magnesium sulfate under the conditions of stirring and heating; and uniformly mixing and then drying, thereby obtaining the powder, namely, the compound chitosan flocculant, wherein the mass ratio of the added chitosan to ferric sulfate to magnesium sulfate is 100:(0.4-0.6):(0.4-0.6). The flocculant is adopted for replacing an organic sulfur treating process and an iron flocculant treating process in an original triple box, so that the treating efficiency for suspended solids can be increased, the dosage of lime can be reduced, the upgrading and reconstruction for the desulfurization waste water are guaranteed, and the dosage of the drugs is reduced.