Integrating MoS2 with various carbonaceous matrices, especially graphene, has been extensively explored for lithium-ion storage. However, mostly reported MoS2/graphene/MoS2 nanostructures have been suffering from their low yield, costly and time-consuming prepared methods as well as their polysulfide shuttling problem owing to a certain degree of adverse reaction to the electrolyte. Herein, layer-by-layer nitrogen-doped graphene/MoS2/nitrogen-doped graphene (NDG/MoS2/NDG) stacking heterostructure has been prepared through a scalable and low-cost in-situ thermal decomposition-reduction method. This new NDG/MoS2/NDG exhibits high crystallization degree MoS2, intimate interface contacts and fully NDG coating, which can effective host the electrochemical products of Mo and soluble lithium polysulfide and restrain the adverse reaction to the electrolyte. As a result, it shows a high initial CE (84.3%), excellent high-rate cycle performance (552 mAh g−1 at 1Ag−1 after 600 cycles) and a high areal capacity (409 mAh g−1 at 8.73mgcm−2) when evaluated as lithium-ion batteries (LIBs) anode. Moreover, we have systematically studied the Li-storage mechanism, which confirms that the NDG coating layer shows significantly effect and advantage on solving polysulfide shuttling problem. We believe that this work can open up an avenue for the rational design of various anode materials, such as NDG coated metal oxides and sulfides for high performance LIBs and other energy related field.