X‐ray fluorescence holography (XFH) is carried out using a synchrotron radiation on CuInSe2 and CuGaSe2 single crystals, which is powerful for the investigation of local atomic structure by three‐dimensional atom image. Incident X‐ray energies (9.7–12.7 keV) are used to excite the Cu Kα fluorescent X‐ray. Atom images are regenerated by Fourier transformation. In the cation plane in CuInSe2 (z = 0), the cation atom spots observed are the 2nd (In), 4th (Cu), 8th (Cu), and 10th (In) – nearest neighbor (NN) of the central Cu atom. For the anion plane (z = c/8) of CuInSe2, Se atoms spots, 1st and 3rd NN of Cu, are observed. Se atom spots are seen to deviate from the regular tetrahedral position due to the bond length difference between Cu‐Se bond and In‐Se bond. In the CuGaSe2 epitaxial layer (300 nm) grown on (100) GaAs, the cation plane exhibits clear atom spots of Cu and Ga atoms up to10th (Ga) NN of Cu. In the anion plane (z = c/8), only 1st NN Se atom spots are observed, and those of 3rd NN atom spots are not been observed. These results are discussed with relation to the perturbation acting on the Se atoms.