Exploring advanced anode materials with highly reversible capacity have gained great interests for large‐scale lithium storage. A facile two‐step method is developed to synthesize nitrogen‐doped carbon coated MoSe2 microspheres via hydrothermal plus thermal polymerization. The MoSe2 microspheres composed of interconnected nanoflakes are homogeneously coated by a thin nitrogen‐doped carbon (N‐C) layer. As an anode for lithium ion batteries, the MoSe2/N‐C composite shows better reversibility, smaller polarization, and higher electrochemical reactivity as compared to the unmodified MoSe2 microspheres. The MoSe2/N‐C electrode delivers a high specific capacity of 698 mAh g−1 after 100 cycles at a current density of 100 mA g−1 and good high rate performance (471 mAh g−1 at a high current density of 2000 mA g−1). The improved electrochemical performance is attributed to the conductive N‐C coating and hierarchical microsphere structure with fast ion/electron transfer characteristics.