The structure of cationic monomers can significantly impact the polarity of lignin after polymerization. Cationic hydrolysis lignin (CHL) polymers were produced by polymerizing hydrolysis lignin (HL) with [3‐(methacryloylamino)propyl] trimethylammonium chloride (MAPTAC) or [2‐(methacryloyloxy)ethyl] trimethyl ammonium chloride (METAC). The METAC monomer has an oxygen atom, with larger electronegativity, in its molecular structure, whereas the MAPTAC monomer contains a nitrogen atom, as well as an extra nonpolar CH2 group, facilitating investigation into the effects of the polarity of CHLs on their physicochemical performance in an aqueous system. CHL polymers are analyzed and their interactions with clay particles are determined in colloidal systems. CHLs are designed to have similar charge densities (2.1–2.2 mmol g−1) and molecular weights (55000–60000 g mol−1 ). The hydrodynamic radius (Hy) and radius of gyration, (Rg) of HL‐METAC are larger than those of HL‐MAPTAC, implying a more 3‐dimensional structure of HL‐METAC in aqueous solution. The stability ratio of kaolin particles affirms the better performance of HL‐METAC in comparison to HL‐MAPTAC, which reflects the better flocculation efficiency of HL‐METAC. The results also reveal that salt and urea aqueous solutions affect the Hy, Rg, and configuration of CHL polymers, which alters the flocculation efficiency of HL‐METAC and HL‐MAPTAC polymers in kaolin suspensions.