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The fine molecular structure of a flocculant fundamentally determines the internal flocculation mechanism and the final application property. In this work, three series of chitosan-based polymers (CTS-g-PAMD) with divergent charge densities and graft chain distribution were synthesized by graft copolymerization using acrylamide (AM) and acryloyloxyethyltrimethylammonium chloride (DAC). Meanwhile, flocculant with linear chain structure (CTS-CTA) was prepared by etherification using 3-chloro-2-hydroxypropyltrimethylammonium chloride (CTA). The characterization results confirmed that various monomers had been successfully introduced into chitosan. The reaction basically happened on —NH 2 at C 2 of chitosan, and the ring structure of chitosan was destroyed by free radical reaction. The obtained flocculants were used to flocculate bentonite and humic acid solution. Besides dose, the effects of chain structure, charge density and chain distribution on flocculation performance were systematically studied. Based on the fractal theory and flocculation kinetics, the effects of structural factors on floc characteristics were also investigated. The results showed that, flocculant with abundant graft chains exerts better flocculation performance and floc characteristic due to enhanced adsorption electrical neutralization and adsorption bridging effect. The effects of charge density and chain distribution on the flocculation performance were disparate in the range of insufficient and excessive doses. Furthermore, on the basis of the quadratic polynomial model, quantitative structure-effect relationships were established, which has guiding significance for the development and utilization of flocculants. Image 1 • Four chitosan-based flocculants with distinct molecular structures were prepared. • The cyclic structure of chitosan was destroyed by graft copolymerization. • Flocculants with "comb" branches exhibited better flocculation performance. • Chain distribution contributed differently under overdose and underdose. • The quantitative structure-activity relationships were established through model. [ABSTRACT FROM AUTHOR]