The use of well-defined materials in heterogeneous catalysis will open up numerous new opportunities for the development of advanced catalysts to address the global challenges in energy and the environment. This review surveys the roles of nanoparticles and isolated single atom sites in catalytic reactions. In the second section, the effects of size, shape, and metal-support interactions are discussed for nanostructured catalysts. Case studies are summarized to illustrate the dynamics of structure evolution of well-defined nanoparticles under certain reaction conditions. In the third section, we review the syntheses and catalytic applications of isolated single atomic sites anchored on different types of supports. In the final part, we conclude by highlighting the challenges and opportunities of well-defined materials for catalyst development and gaining a fundamental understanding of their active sites.