The thermal annealing process is a common treatment used after the preparation step to enhance the electrocatalytic properties of the oxygen reduction reaction (ORR). The structure of a Pt-based bimetallic nanoparticle, which is significantly affected by the catalytic properties, is reconstructed by thermal energy. We investigated the effect of structural reconstruction induced by thermal annealing on the improvement of the ORR using various physical and electrochemical methods. We found that the structural evolution of PtNi nanoparticles, i.e., the Pt-Ni ordering with the Pt shell and the surface reorientation into the (111) facet, is the source of the enhanced ORR activity as well as electrochemical stability through the thermal annealing. This result confirms the crucial factors for the ORR properties by the thermal annealing process and proposes a way to design advanced electrocatalysts.