The ampholytic chitosan based flocculant carboxylated chitosan graft-(3-chloro-2-hydroxypropyl) trimethylammonium chloride-dimethyl diallyl ammonium chloride (CPCTS-g-P (CTA-DMDAAC)) was synthesized by photo polymerization using carboxylated chitosan (CPCTS), 3-chloro-2-chloropropyltrimethylammonium chloride (CTA) and dimethyldiallylammonium chloride (DMDAAC) as the cationic co-monomers. The effects of monomer concentration, the ratio of CPCTS and cationic monomers, cationic degree, initiator time, photoinitiator concentration, and pH value on the properties of CPCTS-g-P (CTA-DMDAAC) were studied. The microcystis aeruginosa that was cultured in laboratory was used for CPCTS-g-P (CTA-DMDAAC) flocculation tests. The effects of CPCTS-g-P (CTA-DMDAAC) dosage, pH value and G value on flocculation performance were investigated. The maximum removal rate of chlorophyll-a (Chl-a) and chemical oxygen demand (COD) that were obtained by CPCTS-g-P (CTA-DMDAAC) were 98.8% and 96.5% under the conditions of dosage 4 mg/L, pH 7 and G value 200 s−1, respectively. The flocculation experiments showed that chitosan-based flocculant CPCTS-g-P (CTA-DMDAAC) had better flocculation performance than commercially available flocculants cationic polyacrylamide (CPAM), Polyferric Sulfate (PFS), and polymeric aluminium (PAC).