To clarify the influence of Ta-substitution on oxygen permeability (JO2) as well as ion conductivity (σi) in a cobaltite perovskite, we investigated detailed crystal structures of (La0.4Sr0.6)(Co1–yTay)O3–δ(y=0.0, 0.1, 0.2) and (La0.4BaxSr0.6–x)(Co0.8Ta0.2)O3–δ (x=0.1, 0.2) at room temperature using synchrotron x-ray powder diffractometry (XRPD). The crystal structure of the (La0.4Sr0.6)(Co1–yTay)O3–δ was modified from cubic (Pm3̅m) to rhombohedral (R3̅c) by substituting Ta ions into perovskite B-sites because the tolerance factor deviates from unity with the Ta-substitutions. The tilting angle ϕ of the CoO6 octahedra and strain parameters η estimated from the refined structural parameters suggest that the crystal structures of the Ta-substituted samples are improved to cubic at elevated temperatures of 800–900°C. Although the lattice volume, the lattice free volume, the O–O bond lengths, and the bottleneck areas gradually increased concomitantly with increasing Ta content, the activation energies estimated from both JO2 and σi increased with Ta-substitution. Results suggest that the electrostatic interaction between Ta5+ and O2− has greater impact than the crystallographic factors for the activation energy increase. Symmetry of the (La0.4BaxSr0.6–x)(Co0.8Ta0.2)O3–δ was improved from rhombohedral (R3̅c) to cubic (Pm3̅m) by substituting Ba ions for the A-sites because the tolerance factor approaches unity. The lattice constant, the O–O bond length, and the bottleneck area increased with the Ba-substitution. The lattice free volume depends on amount ratio between Co3+ and Co4+ cations in the samples. Both JO2 and σi increased with the Ba-substitution. The activation energy Ei of the σi slightly increased with the Ba-substitution.