We compared the catalytic effects of two polymers (soluble starch and apple pectin) on the flocculation of kaolinite suspension. Moreover, the relationship between the zeta potential value and the time when kaolin particle sedimentation occurred was verified, and the mechanism of flocculation was analyzed. Additionally, a constitutive model was proposed to simulate the non-ideal sedimentation of clay particles in an aqueous system under constant gravity. This model not only considers the inhomogeneity of the solute but also simulates the change in clay concentration with time during the deposition process. This model proposes a decay constant (α) and sedimentation coefficient (s). The model can also be used to calculate the instantaneous sedimentation rate of the clay suspensions at any time and any depth for the settling cylinder. These sedimentary characteristics were simulated by adopting the established deposition model. The results show that the model is capable of predicting the time required for the complete sedimentation of particles in the aqueous system, suggesting the feasibility of engineering wastewater treatment, site dredging, etc.