Despite its multidisciplinary interests and technological importance, the shape control of Ru nanocrystals still remains a great challenge. In this article, we demonstrated a facile hydrothermal approach toward the controlled synthesis of Ru nanocrystals with the assistance of first-principles calculations. For the first time, Ru triangular and irregular nanoplates as well as capped columns with tunable sizes were prepared with high shape selectivity. In consistency with the experimental observations and density functional theory (DFT) calculations confirmed that both the intrinsic characteristics of Ru crystals and the adsorption of certain reaction species were responsible for the shape control of Ru nanocrystals. Ultrathin Ru nanoplates exposed a large portion of (0001) facets due to the lower surface energy of Ru(0001). The selective adsorption of oxalate species on Ru(10-10) would retard the growth of the side planes of the Ru nanocrystals, while the gradual thermolysis of the oxalate species would eliminate their adsorption effects, leading to the shape evolution of Ru nanocrystals from prisms to capped columns. The surface-enhanced Raman spectra (SERS) signals of these Ru nanocrystals with 4-mercaptopyridine as molecular probes showed an enhancement sequence of capped columns > triangle nanoplates > nanospheres, probably due to the sharp corners and edges in the capped columns and nanoplates as well as the shrunk interparticle distance in their assemblies. CO-selective methanation tests on these Ru nanocrystals indicated that the nanoplates and nanospheres had comparable activities, but the former has much better CO selectivity than the latter.