The N-doped carbon layer coating MnO microspheres with a core-shell structure (referred as MnO@NC) have been successfully synthesized by combining a facile hydrothermal method with the in-situ interfacial polymerization and subsequent carbonization process in this study. The experimental results manifest that the as-prepared MnO@NC composite exhibits a hierarchical and porous microstructure with better crystallinity and higher specific surface area. When the MnO@NC composite is evaluated as anode materials for lithium ion batteries (LIBs), it can show enhanced electrochemical performances, including the superior cycling performance (784 mAh g−1 after 200 cycles at 500 mA g−1), good rate capacity (206 mAh g−1 at a current density of 4 A g−1) and stable long-term cycling performance (881 mAh g−1 after 250 cycles at a current density of 1 A g−1). The above enhanced electrochemical performances are ascribed to the synergistic effects between the unique microstructure and chemical composition. Therefore, the resultant hierarchical structured porous MnO@NC microspheres could be a promising candidate for the application to the next-generation anode materials in LIBs.