Herein, a chitosan film (CS) was modified using 2,3-epoxy-propyl trimethyl ammonium chloride (GTA) to flocculate granular pollutants in potato starch wastewater, aiming at the deficiencies of poor water solubility and weak electropositivity of the chitosan film. By examining the degree of substitution of chitosan film amino under different factors and different levels and response surface optimization tests, the optimum preparation conditions of chitosan film quaternary ammonium salt (HTCC) were obtained. Using scanning electron microscopy (SEM), Fourier infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and ¹H-nuclear magnetic spectroscopy, the nucleophilic substitution reaction of the GTA molecule with the hydrogen atoms in the chitosan film amino group successfully improved the water solubility and electropositivity of the chitosan film. HTCC was used to treat potato starch wastewater, and the optimal flocculation conditions were obtained. The flocculation product was recovered, and the composition analysis of the flocculation product demonstrated that HTCC-potato protein flocculation precipitate was rich in high protein, which is a good choice of feed and can realize sustainable utilization of resources.