Electrical control of material properties based on ionic liquids (IL) has seen great development and emerging applications in the field of functional oxides, mainly understood by the electrostatic and electrochemical gating mechanisms. Compared to the fast, flexible, and reproducible electrostatic gating, electrochemical gating is less controllable owing to the complex behaviors of ion migration. Here, the interface‐dependent oxygen migration by electrochemical gating is resolved at the atomic scale in the LaAlO
3
–SrTiO
3
system through ex situ IL gating experiments and on‐site atomic‐resolution characterization. The difference between interface structures leads to the controllable electrochemical oxygen migration by filling oxygen vacancies. The findings not only provide an atomic‐scale insight into the origin of interface‐dependent electrochemical gating but also demonstrate an effective way of engineering interface structure to control the electrochemical gating.