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Hierarchical structures in shell with transition metal underneath is a promising design for high-performance and low-cost heterogeneous nanocatalysts (NCs). Such a design enables the optimum extent of synergetic effects in NC surface. It facilitates intermediate reaction steps and, therefore, boosts activity of NC in oxygen reduction reaction (ORR). In this study, carbon nanotube (CNT)-supported ternary metallic NC comprising Cucluster-in-Pdcluster nanocrystal and surface decoration of atomic Pt clusters (14 wt %) is synthesized by using the wet chemical reduction method with sequence and reaction time controls. By annealing in H2 environment (H2/N2 = 9:1, 10 sccm) at 600 K for 2 h, specific activity of Cu@Pd/Pt is substantially improved by ∼2.0-fold as compared to that of the pristine sample and commercial Pt catalysts. By cross-referencing results of electron microscopic, X-ray spectroscopic, and electrochemical analyses, we demonstrated that reduction annealing turns ternary NC into complex of Cu3Pt alloy and CuxPd1–x alloy. Such a transition preserves Pt and Pd in metallic phases, therefore improving the activity by ∼29% and the stability of NC in an accelerated degradation test (ADT) as compared to those of pristine Cu@Pd/Pt in 36 000 cycles at 0.85 V (vs RHE). This study presents robust H2 annealing for structure stabilization of NC and systematic characterizations for rationalization of the corresponding mechanisms. These results provide promising scenarios for facilitation of heterogeneous NC in ORR applications.