The structure, oxygen non-stoichiometry, and defect equilibrium in perovskite-type PrBa1−xSrxFe2O6−δ (x = 0, 0.25, 0.50) synthesized at 1350 °C were studied. For all compositions, X-ray diffraction testifies to the formation of a cubic structure (S.G. ), but an electron diffraction study reveals additional diffuse satellites around each Bragg spot, indicating the primary incommensurate modulation with wave vectors about ±0.43. The results were interpreted as a sign of the short-order in both A-cation and anion sublattices in the areas of a few nanometers in size, and of an intermediate state before the formation of an ordered superstructure. An increase in oxygen deficiency was found to promote the ordering, whereas partial substitution of barium by strontium caused the opposite effect. The oxygen content in oxides as a function of oxygen partial pressure and temperature was measured by coulometric titration, and the data were used for the modeling of defect equilibrium in oxides. The simulation results implied oxygen vacancy ordering in PrBa1−xSrxFe2O6−δ that is in agreement with the electron diffraction study. Besides oxidation and charge disproportionation reactions, the reactions of oxygen vacancy distribution between non-equivalent anion positions, and their trapping in clusters with Pr3+ ions were taken into account by the model. It was demonstrated that an increase in the strontium content in Pr0.5Ba0.5−xSrxFeO3−δ suppressed ordering of oxygen vacancies, increased the binding energy of oxygen ions in the oxides, and resulted in an increase in the concentration of p-type carriers.