We analyze the effect of postdeposition annealing conditions on both the structure and the created defects in Zn0.90Co0.10O thin films, which deposited on the Si(100) substrates by the radio frequency magnetron sputtering technique using a homemade target. The dependence of the number and distribution of defects in homogeneously substituted Co+2 for Zn+2 ions in ZnO lattice on the annealing conditions is investigated. Orientations of thin films are in the  direction with a surface roughness changing from 67 ± 2 nm to 25.8 ± 0.6 nm by annealing. The Co+2 ion substitution, changing from 7.5% ± 0.3% to 8.8 ± 0.3%, leads to the formation of Zn–O–Co bonds instead of Zn–O–Zn bonds and splitting of the Co 2p energy level to Co 2p1/2 and Co 2p3/2 with an energy difference of 15.67 ± 0.06 eV. The defects in the lattice are revealed from the correlations between Zn–O–Co bonds and intensity of the Raman peak at around 691 cm−1. In addition, the asymmetry changes of O 1s peak positions in the x-ray photoelectron spectra are in agreement with the Raman results.