Abstract: Solid–liquid separation is a critical component in treating mineral processing wastewater. Its effectiveness primarily hinges on the disruption of colloidal stability in the wastewater. Flocculants play a key role in destabilizing and dehydrating these colloids. Polyacrylamide is widely utilized as a flocculant in concentrating mills. However, it requires large dosages and contains residual toxic monomers. Developing green, efficient flocculants with multiple active sites is vital for creating an efficient solid–liquid separation process with a low dosage of flocculants, enabling efficient treatment and recycling of mineral processing wastewater. In this work, acrylamide (AM) and dimethyl diallyl ammonium chloride (DMDAAC) are grafted onto the chitosan molecular chain through UV-initiated polymerization, obtaining chitosan-grafted-cationic polyacrylamide (Chi-g-CPAM) with varying molecular structures by modifying the mass fraction of initiator. The chemical structure and crystallinity of the grafted copolymer are characterized using Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectroscopy (¹H NMR), and X-ray diffraction. Chi-g-CPAM’s flocculation performance on kaolinite suspensions is evaluated through settling tests. The adsorption behavior of Chi-g-CPAM on silica surfaces and the flocculation kinetics of kaolinite are investigated using quartz crystal microbalance with dissipation. The adsorption morphology of Chi-g-CPAM on the SiO₂ chip surface, floc structure, and flocculation mechanism are analyzed. The analysis reveals that long branched chains enhance Chi-g-CPAM’s bridging effect on kaolinite, accelerating settling. The abundant branched chains provide substantial positive sites, reducing supernatant turbidity, while short-branched chains result in a "train-like" adsorption conformation on the particle surface of flocculants, weakening the bridging effect. The grafting ratio of Chi-g-CPAM reaches 580.0% at an initiator mass fraction of 0.10%, with numerous long-branched chains. QCM-D measurements indicate that Chi-g-CPAM with these chains exhibits the maximum equilibrium adsorption capacity of (−11.68±0.40) Hz. Initially, a smaller fitting slope of 0.1814 increases to 0.5054 after 509 s, indicating an outward extending adsorption conformation. The flocculation of kaolinite by Chi-g-CPAM is minimal, forming relatively loose flocs. Under the action of Chi-g-CPAM with numerous and long branched chains, the flocculation process is more complicated, as evidenced by the high degree of fit observed in the pseudo-first-order, pseudo-second-order, and Elovich equations. The settling test results reveal that kaolinite suspensions treated by the above flocculant achieve a settling rate of 12.18 m·h^–1, the highest among all tested flocculants. Additionally, the turbidity of the supernatant measures just 13 nephelometric turbidity units, indicating excellent flocculation performance. This is attributed to the synergistic interactions of charge neutralization, bridging, and net-trapping. At initiator mass fraction of 0.15% and 0.05%, the synthesized Chi-g-CPAM with short branched chains exhibits a planar "train-like" adsorption conformation on the SiO₂ surface, which reduces bridging and net-trapping capacity, leading to poor flocculation performance. The molecular structure of multi-active functional flocculants affects their adsorption conformation on mineral surfaces, a critical factor in determining their flocculation performance. The findings of this study offer valuable insights into the molecular structure design of macromolecular agents for mineral processing.