A new reconstruction technique for X‐ray fluorescence hologram data was proposed based on extractions of holographic oscillations from single scatterers within a sample. The extractions were iteratively carried out by the inverse Fourier transformation of selected atomic images, which were obtained by the Fourier transformation of one‐dimensional hologram averaged over azimuth about a given polar axis in k‐space. The refinement of the real space reconstruction was performed using the measured holograms and the extracted holographic oscillations. I applied this data processing to the theoretical holograms of fcc Au cluster at 12.0, 12.5 and 13.0 keV, and successfully obtained clear atomic image without artifacts.