Carbon-supported nanoparticles have been used widely as efficient catalysts due to their enhanced surface-to-volume ratio. To investigate their structure–property relationships, acquiring 3D elemental distribution is required. Here, carbon-supported Pt, PtMn alloy, and ordered Pt3Mn nanoparticles are synthesized and analyzed with atom probe tomography as model systems. A significant difference of Mn distribution after the heat-treatment was found. Finally, the field evaporation behavior of the carbon support was discussed and each acquired reconstruction was compared with computational results from an evaporation simulation. This paper provides a guideline for studies using atom probe tomography on the heterogeneous carbon-supported nanoparticle system that leads to insights toward a wide variety of applications.