The effect of the interfacial energy on the electric-field-induced sphere-to-cylinder (S-to-C) transition in poly styrene-b-poly(methyl methacrylate) (PS-b-PMMA) copolymer thin films was studied as a function of the difference in the interfacial interactions of the PS and PMMA blocks with the substrate, delta. It was found that the interfacial energies altered both the critical electric field strength and the time scales of kinetics. A very strong preferential interfacial interaction suppressed the electric-field-induced S-to-C transition even though such a transition occurred on a neutralized surface where the interfacial interactions were balanced. For a moderate interfacial interaction, the S-to-C transition can be induced by an applied electric field, but the time scale of the morphology change is much longer. Furthermore, the formation of ionic complexes in the BCP was found to enhance the electric-field-induced S-to-C transition even on a native Si substrate without any surface modification, providing a simple route to generate ordered arrays of high-aspect-ratio cylinders oriented normal to a film surface.