We report on the effect of oxygen deficiency on the structural and magnetic properties of Ba(Co 1%x Mn x )O 3 (x = 0.10-0.20) ceramics, as characterized by synchrotron X-ray spectroscopy. Different amounts of oxygen deficiency were introduced by an annealing process under vacuum. The stoichiometry of the oxygen ions in the ceramic samples gradually decreased from an ABO 3 -perovskite type to an ABO 2 type with increasing annealing temperature. Saturation magnetization decreased with increasing annealing temperature irrespective of the amount of Mn substitution, and the magnetic properties for the x = 0.10-0.20 samples changed from ferromagnetic to paramagnetic. According to the X-ray photoelectron spectroscopy (XPS) using synchrotron X-ray radiation and X-ray absorption near-edge structure (XANES) spectroscopy measurements for the x = 0.10 samples, the valence states of the Co and Mn ions gradually changed from tetravalent to trivalent to divalent with increasing annealing temperatures. The transient states of the structural and magnetic properties owing to the induced oxygen deficiency could be observed by synchrotron X-ray spectroscopy.