Recently, more attentions have been paid to natural polymer-based flocculants in water treatment, since they are believed to be low-cost, nontoxic, and environmentally friendly materials. In this work, strong cationic chitosan-based graft copolymer flocculants (3-chloro-2-hydroxypropyl trimethyl ammonium chloride (CTA) modified chitosan-graft-polyacrylamide, denoted as chitosan-CTA-g-PAM) have been prepared, and their flocculating properties were studied systematically, both at the laboratory scale and at the pilot scale. In laboratory scale, a kaolin suspension was employed as synthetic wastewater. The effects of dosage, temperature, and original turbidity of untreated wastewater were investigated, respectively. Moreover, in pilot scale, the raw water from the Zhenjiang part of the Yangtse River in China was used as wastewater. The influences of three external factors-dosage, sedimentation time, and mechanical mixing rate on the flocculating performances have been studied by orthogonal testing, respectively. The experimental results in pilot scale were fairly consistent with those from the beaker experiment in laboratory scale. In comparison with polyferric sulfate, which is the flocculant currently used by the Zhenjiang Water Supply Company, chitosan-CTA-g-PAM showed better flocculating properties. Meanwhile, the effect of the degree of substitution of CTA on the flocculating properties has been also studied, both at the laboratory scale and at the pilot scale. It was indicated that chitosan-CTA-g-PAM with higher cationic degree had better flocculating performances, which was also confirmed by the flocculation kinetics analysis. Furthermore, the flocculation mechanisms of chitosan-CTA-g-PAM have been discussed in detail. Above all, the flocculating experiments in laboratory and pilot scales both indicated that chitosan-CTA-g-PAM showed good flocculating performances in water treatment.