Ferroelectric barium titanate nanoparticles (BTO NPs) may play critical roles in miniaturized passive electronic devices such as multi-layered ceramic capacitors. While increasing experimental and theoretical understandings on the structure of BTO and doped BTO have been developed over the past decade, the majority of the investigation was carried out in thin-film materials; therefore, the doping effect on nanoparticles remains unclear. Especially, doping-induced local composition and structure fluctuation across single nanoparticles have yet to be unveiled. In this work, we use electron microscopy-based techniques including high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), integrated differential phase contrast (iDPC)-STEM, and energy dispersive X-ray spectroscopy (EDX) mapping to reveal atomically resolved chemical and crystal structure of BTO and strontium doped BTO nanoparticles. Powder X-ray diffraction (PXRD) results indicate that the increasing strontium doping causes a structural transition from tetragonal to cubic phase, but the microscopic data validate substantial compositional and microstructural inhomogeneities in strontium doped BTO nanoparticles. Our work provides new insights into the structure of doped BTO NPs and will facilitate the materials design for next-generation high-density nano-dielectric devices.