Electrokinetic remediation (EKR) is a promising alternative for the contaminated soil with low hydraulic permeability. The nonlinearity of the electroosmotic flow (EOF) is mainly induced by the nonuniform variation of the pH and thus the zeta potential of the soil during the EKR process. The empirical relation between the zeta potential and the pH for kaolinite is currently applied to analyze the nonlinearity of the EOF. A new perspective for theoretical determination of the zeta potential for the variable charge soil is proposed in this study. The prediction model incorporates the pH, the valence and concentration of the electrolyte, and the temperature and permittivity of the solvent surrounding the clay particles. Satisfying agreement between the calculated and measured curves of zeta potential versus pH for three types of variable charge soil was achieved. This model would act as a useful tool to simulate the nonlinearity of the electroosmosis of the variable charge soil and provide guidance and precise control mechanism for maximizing the efficiency of the EOF.