© 2019 The Japan Society of Applied Physics. This study experimentally investigated the atomic structure of a single-crystalline Mn-doped BiFeO3 (BFO) thin film using X-ray fluorescence holography with synchrotron radiation. Bi atoms can be reconstructed from both Fe Kβ and Mn Kα fluorescence X-ray holograms, indicating Mn doping at B sites in ABO3-type perovskite structure. The fluorescence intensity of the 1st to 4th nearest Bi atoms around target Fe atoms was lower than those around Mn atoms, confirming the selective formation of Bi vacancies around Fe atoms. In contrast, the 5th to 8th nearest Bi atoms around Fe atoms showed higher intensities than those around Mn atoms, indicating that the Mn-doped BFO thin film had a double-perovskite-like structure. These results provide important information that helps elucidate the mechanism by which Mn doping modifies the conductivity of BFO.