Rational design of advanced electrode materials is extremely important for high-performance lithium-ion batteries (LIBs). Herein, we report a facile one-pot hydrothermal approach for formation of MoS2/nitrogen-doped graphene (MoS2/N-graphene) composite with excellent lithium storage properties as anode for LIBs. The controlled experiment results indicate that polyethyleneimine (PEI) functionalizes not only as the nitrogen source for in-situ nitrogen doping, but also as a binder for inducing and regulating the uniform growth of MoS2 nanosheets onto graphene. As a result, ultrathin MoS2 nanosheets are vertically grown onto the nitrogen-doped reduced oxide graphene (RGO), generating a distinct honeycomb-like hybrid structure. More significantly, the first principles theoretical calculations results manifest that there is a strong interaction at the interface of MoS2 and nitrogen-doped graphene, thus boosting the charge transfer. The constructing MoS2/N-graphene architecture demonstrates the improved electrochemical performances for reversible lithium storage. It shows a high reversible capacity of 1025.1 mAh/g at a current density of 100 mA/g and the superior rate capability, which is mainly attributed to the pseudocapacitance contributions.