High-performance lithium and sodium ion batteries typically consist of heterogeneous composite electrode materials that integrate different components and are used for a variety of structural and electrochemical functions. Designing heterogeneous composite electrode materials to significantly enhance battery performance depends on the basic understanding of the mechanisms and synergistic effects of different components. In this work, we develop a simple design and preparation of heterostructured hollow ZnSnO3@carbon microcubes composite (denoted as H-ZnSnO3@C), consisting of a ZnSnO3 microcube within hollow structure surrounded by the thin carbon coating shell. Meaningfully, the H-ZnSnO3@C electrode shows desirable cycle stability (100 cycles, 817 mAh g−1 at 0.1 A g−1) for lithium storage. Moreover, a charge capacity of 302 mAh g−1 is obtained for sodium storage. By systematic electrochemical analysis, we elucidate that the inner hollow space can effectively sustain the lithiation/sodiation-induced expansion of ZnSnO3 without breaking the outer carbon coating shells and the conductive outer carbon shells allow for a fast electron conduction as well as limit most SEI formation to the carbon surface instead of on the ZnSnO3-electrolyte interface, thus enhancing the rate performance. More importantly, the electrochemical kinetics analysis and density functional theory calculations confirms the basic principles of enhanced electrochemical performance. This work indicates an effective method of engineering the metal oxide-carbon heterogeneous composite as advanced electrodes for energy storage devices.