Due to the limited exploitation and utilization of fossil energy resources in recent years, it is imperative to explore and develop new energy materials. As an electrode material for batteries, MnCO3 has the advantages of safety, non-toxicity, and wide availability of raw materials. But it also has some disadvantages, such as short cycle period and low conductivity. In order to improve these deficiencies, we designed a MnCO3@Mn3O4 heterostructure material by a simple solvothermal method, which possessed a microstructure of “butterfly-tie”. Owing to the introduction of Mn3O4 and the layered structure of “butterfly-tie”, MnCO3@Mn3O4 possessed a discharge capacity of 165 mAh/g when the current density was 0.2 A/g and exhibited satisfactory rate performance. The MnCO3@Mn3O4 heterostructure was optimized by density functional theory (DFT), and the deformation charge density was calculated. It was found that the MnCO3@Mn3O4 heterostructure is stable owing to the molecular interaction between the O atoms from MnCO3 and the Mn atoms from Mn3O4 at the interface of heterojunction. Therefore, the MnCO3@Mn3O4 heterostructure material has promising applications as safe and efficient cathode material for energy batteries.