To develop high-performance anode materials of lithium ion batteries (LIBs) for practical high energy application, a grain boundaries enriched hierarchically mesoporous MnO/C microsphere composite has been fabricated by an in-situ carbonization process. The mesoporous MnO/C microsphere is constructed by abundant grains and grain boundaries that are uniformly embedded in a carbon matrix. Such unique nanoarchitecture exhibits high tap density and structural stability, and provides 3D continuous transport pathways for electrons and Li-ions, enabling high electrochemical stability and improved lithium storage kinetics. As a consequence, the mesoporous MnO/C electrode delivers ever-increasing specific capacity (1200mAhg−1 after 100 cycles at 100mAg−1) and excellent rate capability (588mAhg−1 at 2Ag−1). Such superior lithium storage performance suggests that the hierarchically mesoporous MnO/C microsphere electrode should be one of the most promising anode materials for electric vehicle and grid energy storage application.