Metallic materials are usually composed of single phase or multiple phases, which refers to homogeneous regions with distinct types of the atom arrangement. The recent studies on nanostructured metallic materials provide a variety of promising approaches to engineer the phases at the nanoscale. Tailoring phase size, phase distribution, and introducing new structures via phase transformation contribute to the precise modification in deformation behaviors and electronic structures of nanostructural metallic materials. Therefore, phase engineering of nanostructured metallic materials is expected to pave an innovative way to develop materials with advanced mechanical and functional properties. In this review, we present a comprehensive overview of the engineering of heterogeneous nanophases and the fundamental understanding of nanophase formation for nanostructured metallic materials, including supra-nano-dual-phase materials, nanoprecipitation- and nanotwin-strengthened materials. We first review the thermodynamics and kinetics principles for the formation of the supra-nano-dual-phase structure, followed by a discussion on the deformation mechanism for structural metallic materials as well as the optimization in the electronic structure for electrocatalysis. Then, we demonstrate the origin, classification, and mechanical and functional properties of the metallic materials with the structural characteristics of dense nanoprecipitations or nanotwins. Finally, we summarize some potential research challenges in this field and provide a short perspective on the scientific implications of phase engineering for the design of next-generation advanced metallic materials.