A micro-scale rod-like heterostructure derived from molybdenum-based metal organic framework (Mo-MOF) has been successfully prepared via subsequent annealing treatment, which assembled from N-doped carbon encapsulated MoSe2 nanosheets grown on the surface of MoO2 microrod (named as MoO2@MoSe2@NC). For this novel heterostructure, the MoO2 nanoparticles assembled into rod core not only serve as supporting substrate for facilitating the fast kinetics of Li+ cations inside the electrode but also protect the MoSe2 structure from restacking in the charge/discharge process. Moreover, the outer-layered MoSe2 nanosheets enable the fast lithium ion movement owing to its large interlayer spacing. Moreover, this unique rod-like core–shell structure composite could further effectively alleviate the structural strains caused by large volume expansion during charge/discharge process, thus leading to stable electrochemical performance when evaluated as anode material for lithium ion batteries. Electrochemical testing exhibits that the MoO2@MoSe2@NC heterostructure presents highly reversible capacity of 468 mAh g−1 at 0.5 A g−1 and superior rate capability (318 mAh g−1 even at 5.0 A g−1), which is attributed to the synergistic effect of N-doped carbon encapsulated MoSe2 nanosheets and MoO2 nanoparticles.