Defects in perovskite oxide solid electrolytes (SEs) impact Li-ion conductivity. However, the role of oxygen vacancies (Vo) in transport behavior has been less explored. Herein, our study elucidates the microscopic origin of the role of Vo in enhancing the total ionic conductivity of a prototype lithium lanthanum titanate while maintaining its insulating properties. Scanning transmission electron microscopy and theoretical calculations reveal that the presence of Vo significantly lowers the activation energy of Li-ion migration. The Vo is revealed to be preferentially aligned parallel to c-planes and causes modulated lattice expansion in an alternating manner, resulting in easy directional Li-ion transport. The effect of Vo-assisted Li-ion transport is optimized through the hierarchical rearrangement of structural features at multiple length scales close to the direction of the Vo arrays. Our results offer novel insights into the microscopic origins of superior ion conductivity facilitated by Vo, contributing to the design of high-performance SEs.