To fabricate intermetallic nanoparticles with high oxygen reduction reaction activity, a high-temperature heat treatment of 700 to 1,000 °C is required. This heat treatment provides energy sufficient to induce an atomic rearrangement inside the alloy nanoparticles, increasing the mobility of particles, making them structurally unstable and causing a sintering phenomenon where they agglomerate together naturally. These problems cannot be avoided using a typical heat treatment process that only controls the gas atmosphere and temperature. In this study, as a strategy to overcome the limitations of the existing heat treatment process for the fabrication of intermetallic nanoparticles, we propose an interesting approach, to design a catalyst material structure for heat treatment rather than the process itself. In particular, we introduce a technology that first creates an intermetallic compound structure through a primary high-temperature heat treatment using random alloy particles coated with a carbon shell, and then establishes catalytic active sites by etching the carbon shell using a secondary heat treatment process. By using a carbon shell as a template, nanoparticles with an intermetallic structure can be kept very small while effectively controlling the catalytically active area, thereby creating an optimal alloy catalyst structure for fuel cells.