Fe Kα X-ray fluorescence holography measurements were carried out at room temperature on an FeSe high-temperature superconductor to clarify the relationship between the local structures around the Fe atoms and the superconducting nature. The obtained three-dimensional atomic arrangements strongly reveal a formation of strong FeSe4 clusters. On the other hand, the Se—Fe—Se bond angle largely spreads, causing a large ambiguity in the chalcogen height and large displacements of the Fe sublattice. Thus, it is reasonable that the tetragonal-to-orthorhombic structural (nematic) transition does not affect the magnetic ordering in the Fe layer.