The d-band-filling of transition metals in complex oxides plays an essential role in determining their structural, electronic and magnetic properties. Traditionally, at the oxide heterointerface, band-filling control has been achieved via electrostatic modification in the structure of field-effect transistors or electron transfer, which is limited to the quasi-two-dimension at the interface. Here we report a three-dimensional (3D) band-filling control by changing the local lattice coordination in a designed oxide heterostructure. At the LaCoO3/LaTiO3 heterointerface, due to the Fermi level mismatch, electrons transfer from LaTiO3 to LaCoO3. This triggers destabilisation of the CoO6 octahedrons, i.e. the formation of lattice configurations with a reduced Co valence. The associated oxygen migration results in the 3D topotactic phase transition of LaCoO3. Tuned by the thickness of LaTiO3, different crystalline phases and band-fillings of Co occur, leading to the emergence of different magnetic ground states.