Controllable synthesis of metallic nanocrystals (NCs) with tunable phase, uniform shape, and size is of multidisciplinary interests but has still remained challenging. Herein, a robust phase control strategy is developed, in which seeds with a given phase are added to guide the epitaxial growth of the target metal to inherit the seeds’ phase. Through this strategy, M@Ru (M = Pt, Pd) NCs in the face-centered cubic (fcc) phase, a metastable phase for Ru under ambient conditions, were synthesized with the hydrothermal method. The Pt@Ru NCs showed not only the pure fcc phase but also high morphology selectivity to tetrahedrons surrounded by {111} facets. As revealed by density function theory (DFT) calculations, the preferentially epitaxial growth of Ru atom layers on the nonclosest-packed facets of hetero fcc metal seeds led to the formation of fcc Ru shells. Furthermore, the fcc Pt@Ru tetrahedrons/C showed electrocatalytic activity enhancement with more than an order of magnitude toward hydrogen oxidation reaction (HOR) in acidic electrolyte compared with hydrothermally synthesized Ru/C. Electrochemical measurement combined with DFT calculations revealed that the optimum HOR activity should be achieved on well-crystallized fcc Ru catalysts exposing maximum {111} facets.