The negative uniaxial magnetocrystalline anisotropy (K_u) was evaluated for various compositions of Co_100−xIr_x thin films with respect to the atomic layer stacking structure. Pure Co film fabricated at a substrate temperature (T_sub) of 600 ℃ was found to have a positive K_u of 6.1×10⁶ erg/cm³. With increasing x, the sign of K_u changed from positive to negative, and the negative K_u took a maximum value of −9.6×10⁶ erg/cm³ at around x = 20 at. % for films fabricated at T_sub = 600 ℃. Adding more Ir decreased the absolute value of the negative K_u which became 0 over x = 50 at. %. X−ray diffraction analysis and scanning transmission electron microscopy revealed that the atomic layer stacking structure of the Co_100−xIr_x films changed from −A−B−A−B− (hcp) to −A−B−C−A−B−C− (fcc) stacking with increasing Ir content. Moreover, Co₈₀Ir₂₀ grains were revealed to consist of 2 kinds of randomly located composition−modulated atomic layers, nearly pure−Co and pure−Ir layers, while Co and Co₅₀Ir₅₀ had disordered structures. In this paper, a new perspective on the atomic layered structure with superlattice diffraction, which is different from the conventional “ordered structure”, is discussed.