The oxygen nonstoichiometry in the misfit calcium cobaltite (Ca2CoO3)0.62(CoO2) has been studied experimentally and by density functional theory (DFT) calculations. The standard oxidation enthalpy ΔH0Ox of oxygen deficient (Ca2CoO3)0.62(CoO2) was measured directly using simultaneous thermogravimetry and differential scanning calorimetry. ΔH0Ox was found to be in agreement with the prediction from a previously published defect chemical model based on purely thermogravimetrical analysis. A series of samples with different oxygen vacancy concentration was prepared by annealing in air, followed by rapid quenching. Room-temperature Raman spectroscopy showed a sharp mode at 700 cm–1 decreasing in intensity with increasing vacancy concentration. We discuss this observation as evidence for oxygen vacancies being preferably formed within the central layer of the Ca2CoO3 subsystem. DFT calculations demonstrated that the calculated electronic structure is sensitive to the chosen model of the crystal structure. Still, for all investigated models, the standard formation enthalpy of oxygen vacancies within the Ca2CoO3 moiety was much lower than that for a site within the CoO2 layer, in agreement with the presented experimental data.