Noble metal nanocrystals own high chemical stability, unique plasmonic and distinctive catalytic properties, making them outstanding in many applications. However, their practical applications are limited by their high cost and scarcity on the earth. One promising strategy to solve these problems is to boost their catalytic performance in order to reduce their usage amount. To realize this target, great research efforts have been devoted to the size-, composition-, shape- and/or architecture-controlled syntheses of noble metal nanocrystals during the past two decades. Impressively, recent experimental studies have revealed that the crystal structure of noble metal nanocrystals can also significantly affect their physicochemical properties, such as optical, magnetic, catalytic, mechanical, electrical and electronic properties. Therefore, besides the well-established size, composition, shape, and architecture control, the rise of crystal structure-controlled synthesis of noble metal nanocrystals will open up new opportunities to further improve their functional properties, and thus promote their potential applications in energy conversion, catalysis, biosensing, information storage, surface enhanced Raman scattering, waveguide, near-infrared photothermal therapy, controlled release, bioimaging, biomedicine, and so on. In this Account, we review the recent research progress on the crystal structure control of noble metal nanocrystals with a template synthetic approach and their crystal structure-dependent catalytic properties. We first describe the template synthetic methods, such as epitaxial growth and galvanic replacement reaction methods, in which a presynthesized noble metal nanocrystal with either new or common crystal structure is used as the template to direct the growth of unusual crystal structures of other noble metals. Significantly, the template synthetic strategy described here provides an efficient, simple and straightforward way to synthesize unusual crystal structures of noble metal nanocrystals, which might not be easily synthesized by commonly used chemical synthesis. To be specific, by using the epitaxial growth method, a series of noble metal nanocrystals with unusual crystal structures has been obtained, such as hexagonal close-packed Ag, 4H Ag, Pd, Pt, Ir, Rh, Os, and Ru, and face-centered cubic Ru nanostructures. Meanwhile, the galvanic replacement reaction method offers an efficient way to synthesize noble metal alloy nanocrystals with unusual crystal structures, such as 4H PdAg, PtAg, and PtPdAg nanostructures. We then briefly introduce the stability of noble metal nanocrystals with unusual crystal structures. After that, we demonstrate the catalytic applications of the resultant noble metal nanocrystals with unusual crystal structures toward different chemical reactions like hydrogen evolution reaction, hydrogen oxidation reaction and organic reactions. The relationship between crystal structures of noble metal nanocrystals and their catalytic performances is discussed. Finally, we summarize the whole paper, and address the current challenges and future opportunities for the template synthesis of noble metal nanocrystals with unusual crystal structures. We expect that this Account will promote the crystal structure-controlled synthesis of noble metal nanocrystals, which can provide a new way to further improve their advanced functional properties toward their practical applications.