NaInO2 and NaInS2 with α-NaFeO2 layer type structure have been prepared and characterized by X-ray photoelectron spectroscopy to clarify the role of the anions in the electronic structures of the compounds. The In 3d5/2 binding energy for both compounds was the same, though the Na1s binding energy of NaInO2 was larger than that of NaInS2 by 0.4 eV. The change in the Na Auger parameter, defined as the sum of Na1s binding energy and KLL Auger kinetic energy, suggests that the difference in extra-atomic relaxation energy between the compounds causes the Na1s binding energy shift. Discrete variational-Xα model cluster calculations for NaInO2 and NaInS2 mirrored the experimental valence band spectra and the difference of 0.5 eV in optical absorption energy of the compounds. The cluster calculation revealed that in NaInO2 the highest occupied level is formed by an antibonding Na–O bond, whereas that in NaInS2 is formed by a bonding Na–S bond. The covalent Na–S bond decreases the extra-atomic relaxation energy for Na1s electron emission from NaInS2.