Abstract: Mineral processing requires considerable quantities of water. Efficient treatment of mineral processing wastewater is essential for sustainable mining development. Chitosan is a linear cationic polysaccharide polymer derived from chitin via deacetylation. It exhibits advantages including low cost, non-toxicity, and biodegradability. Chitosan is considered the most promising green flocculant; however, its low molecular weight and poor solubility limit its application. Chemical modification can enhance the physicochemical properties of chitosan. Graft copolymerization is an effective method to improve the water solubility and flocculation performance of chitosan. In this study, to develop green and efficient chitosan-based flocculants and improve the treatment efficiency of mineral processing wastewater, different types of chitosan graft copolymers were constructed based on the molecular dynamics simulation method: non-ionic chitosan grafted polyacrylamide (Chi-g-PAM), cationic chitosan grafted acrylamide-dimethyl diallyl ammonium chloride (Chi-g-P(AM-DMDAAC)), and anionic carboxymethyl chitosan grafted polyacrylamide (CMC-g-PAM). By calculating solvation free energy (ΔG_SFE), radius of gyration (R_g), mean square displacement (MSD), and diffusion coefficient (D), the effects of graft monomer type on the solubility of chitosan graft copolymers were systematically analyzed. Specifically, ΔG_SFE, R_g, MSD, and D of CMC-g-PAM and Chi-g-P(AM-DMDAAC) were significantly higher than those of Chi-g-PAM. The results indicated that, compared with non-ionic flocculants, ionization of ionic flocculants increased interaction force between the flocculant and water molecules and generated electrostatic repulsion between polymer chains, enhancing chain extension and solubility. The cationic Chi-g-P(AM-DMDAAC) with good water solubility was selected as the research object. The adsorption capacity of Chi-g-P(AM-DMDAAC) was characterized by interaction energy (E_interaction); its bridging ability was evaluated based on solvent accessible surface area (SASA), R_g, MSD, D, and adsorption conformation. The effects of the number and length of branched chains on the flocculation performance of chitosan graft copolymers were analyzed in detail. The results indicated that, as the number and length of chitosan branches increased from 2/3 to 6/9, E_interaction, R_g, SASA, and D values exhibited an upward trend, whereas adsorption conformation transitioned from a “train-like” adsorption to a configuration where one end of the flocculant adsorbed onto the kaolinite interface and the other end fully extended into the aqueous phase, yielding optimal flocculation performance. When the number of branches continued to increase but their length decreased, E_interaction, R_g, SASA, and D values diminished, reducing flocculation efficiency. To verify molecular dynamics calculations, Chi-g-P(AM-DMDAAC) with different numbers and lengths of branched chains was synthesized by varying initiator concentration. The flocculation effects of Chi-g-P(AM-DMDAAC) with different numbers and lengths of branched chains on kaolinite particles were investigated using kaolin suspension as the object. The results showed that the flocculant with a large number of long-branched chains exhibited the maximum initial sedimentation rate and could effectively neutralize negative charge on the surface of kaolin, which was consistent with simulation results. This study provides a critical foundation for developing green and efficient chitosan-based flocculants and offers valuable guidance for selecting flocculants in mineral processing wastewater treatment.