Controlling the polymorphism of metal nanocrystals is a promising strategy for enhancing properties and discovering new phenomena. However, previous studies on Rh nanocrystals have focused on their thermodynamically stable face-centered-cubic (fcc) phase. Herein, a facile synthesis of Rh-based nanocrystals featuring the metastable hexagonal close-packed (hcp) phase is reported by using Ru seeds in their native hcp phase to template the deposition of Rh atoms. The success of such phase-controlled synthesis relies on the templating effect promoted by the small lattice mismatch between Ru and Rh and the slow dropwise titration of the precursor at an elevated temperature, ensuring the layer-by-layer growth mode and thus the formation of a conformal hcp-Rh shell. Faster injection rate of Rh(III) precursor leads to the formation of a rough Rh shell in the conventional fcc phase due to accelerated reaction kinetics. Considering both thermodynamic and kinetic aspects of this system, the hcp-Rh phase is favored when the low surface energy from smooth overlayers balances the high bulk energy of the metastable phase, achieved through tight control of reaction rates and deposition patterns. These Ruhcp@Rhhcp core-shell nanocrystals demonstrate thermal stability up to 400°C, while exhibiting higher catalytic activity toward ethanol oxidation reaction compared to Ruhcp@Rhfcc counterparts.