Advanced anode materials for lithium ion batteries are central to the area of electrical energy storage devices. Herein, we have developed a two-step strategy for synthesizing MoS2@polypyrrole (MoS2@PPY) core-shell microspheres. In such a novel architecture, the MoS2 microspheres are homogeneously wrapped by conductive polypyrrole coating forming core-shell microspheres. As a preliminary test, the obtained MoS2@PPY microspheres exhibit greatly enhanced electrochemical performances for lithium storage compared with un-modified MoS2 microspheres. The MoS2@PPY microsphere electrode displays a high specific capacity of 1012 mAh g−1 after 200 cycles at 200 mA g−1 and high rate performance (600 mAh g−1 at 4000 mA g−1). The superior electrochemical performances are attributed to the advantageous combination of hierarchical microsphere structure and conductive PPY coating.