The search for a low-cost, ultrastable, and highly efficient non-precious metal catalyst substitute for Pt in the oxygen reduction reaction (ORR) is extremely urgent, especially in acidic media. Herein, we develop a template-assisted pyrolysis (TAP) method to obtain a unique Co catalyst with isolated single atomic sites anchored on hollow N-doped carbon spheres (ISAS-Co/HNCS). Both the single sites and the hollow substrate endow the catalyst with excellent ORR performance. The half-wave potential in acidic media approaches that of Pt/C. Experiments and density functional theory have verified that isolated Co sites are the source for the high ORR activity because they significantly increase the hydrogenation of OH* species. This TAP method is also demonstrated to be effective in preparing a series of ISAS-M/HNCS, which provides opportunities for discovering new catalysts.