In capillary electrochromatography with the mixed-mode stationary phase, while the transfer of solutes could be controlled by the contributions of chromatography (reversed-phase and ion exchange), the transfer of charged solutes could be influenced by electrophoresis transfer. According to the principle of ion independent transfer and several kinds of interaction between solute, mobile phase, and stationary phase, an theoretical expression was derived to describe the relationship among the apparent transfer velocity of solute, the transfer velocities in various forms and the diversified interactions. The studies focused on the influence of various parameters (e.g., pH, organic modifier content, stationary phase proportion) and the transfer characters of various solutes in the mixed-mode capillary electroosmotic chromatography (CEC). These results demonstrate that electroosmotic flow in the mixed stationary phase electrochromatography are kept high and steady within wide ranges of pH and organic modifier content. The separation was affected by the pH through the change of the solutes conformation. The influence of neutral solutes by organic modifier complies with the rule of conventional reversed-phase CEC. The separation of charged solutes was influenced evidently by the compete reagents which could improve the shape of the peak, but it was not so important as in the conventional ion exchange chromatography due to the adjustment by the function of electrophoresis.