Electrochemical shape-controlled synthesis of metal nanocrystal (NC) catalysts bounded by high-index facets with high surface energy was achieved by developing a square-wave potential route. Tetrahexahedral Pt NCs with 24 {hk0} facets, concave hexoctahedral Pt NCs with 48 {hkl} facets, and multiple twinned Pt nanorods with {hk0} facets were produced. The method was employed also to synthesize successfully trapezohedral Pd NCs with 24 {hkk} facets, and concave hexoctahedral Pd NCs with 48 {hkl} facets. It has been tested that, thanks to the high-index facets with high density of atomic steps and dangling bonds, the tetrahexahedral Pt NCs exhibit much enhanced catalytic activity for equivalent Pt surface areas for electrooxidation of small organic fuels such as ethanol. These results demonstrate that the developed square-wave potential method has surmounted the limit of conventional chemical methods that could synthesize merely metal nanocrystals with low surface energy, and opened a new prospect avenue in shape-controlled synthesis of nanoparticle catalysts with high surface energy and enhanced activity.