Although Mn-based composites are promising anode materials for advanced lithium-ion batteries (LIBs) owning to their high theoretical capacity (about 2–4 times of commercial graphite), they have some practical limitations such as poor electronic conductivity and large volume expansion, which leading to poor cycle performance. Herein, we developed a versatile strategy to synthesize porous structured MnO/Mn3O4 submicrospheres encapsulated by N-doped carbon shell (MnO/Mn3O4@NC) through an efficient annealing treatment. The as-prepared MnO/Mn3O4@NC composite delivered an excellent electrochemical performance, including a high reversible capacity of 990mAhg−1 at 0.2 A g−1 over 100cycles and superior rate capability. The outstanding electrochemical performance of MnO/Mn3O4@NC could be attributed to its porous structure and the well-defined protection by N-doped carbon shell for facilitating the transport of electrons and alleviating the volume expansion.