Colloidal probe atomic force microscopy (CP-AFM) can be used for measuring force curves between the colloidal probe and the substrate in a colloidal suspension. In the experiment, an oscillatory force curve reflecting the layer structure of the colloidal particles on the substrate is usually obtained. However, the force curve is not equivalent to the interfacial structure of the colloidal particles. In this paper, the force curve is transformed into the number density distribution of the colloidal particles as a function of the distance from the substrate surface using our newly developed transform theory. It is found by the transform theory that the interfacial stratification is enhanced by an increase in an absolute value of the surface potential of the colloidal particle, despite a simultaneous increase in a repulsive electrostatic interaction between the substrate and the colloidal particle. To elucidate the mechanism of the stratification, an integral equation theory is employed. It is found that crowding of the colloidal particles in the bulk due to the increase in the absolute value of the surface potential of the colloidal particle leads to pushing out some colloidal particles to the wall. The combined method of CP-AFM and the transform theory (the experimental theoretical study of the interfacial stratification) is related to colloidal crystallization, glass transition, and aggregation on a surface. Thus, the combined method is important for developments of colloidal nanotechnologies.