Fe 5−x GeTe 2 is a two-dimensional van der Waals material that exhibits ferromagnetic order with a high Curie temperature (T C ) of around room temperature. In addition to T C , two magnetic transitions occur with decreasing temperature, and a charge-ordered state is observed at low temperatures. We employed Ge Kα X-ray fluorescence holography (XFH) for Fe 5−x GeTe 2 to directly investigate the local structure in the charge-ordered state, i.e., the × 3 3 superstructure. The Ge Kα XFH results revealed local atomic structures around the Ge atom, thus clarifying the simultaneous locations and arrangements of the Te, Fe, and Ge atoms. The atomic positions relative to the Ge atom are useful for understanding the coexistence of the ideal 1 × 1 structure and × 3 3 superstructure found in the chargeordered state.