MoS2 is a potential Li storage material that can be used as lithium-ion battery anodes, but its inherent low conductivity and volume expansion in cycling constrain its usefulness. Here, nanoflower-like MoS2@NC@CNT composites containing nitrogen-doped carbon-coated MoS2 nanosheets and CNTs were prepared, presenting decreased charge transfer resistance, increased Li+ diffusion rate and high structural stability to resist volume expansion of MoS2. The coating of nitrogen-doped carbon reinforces the stability of the structure by increasing the compactness and lowering the dimension of the MoS2 nanosheets, and it also compensates for the limited conductivity of MoS2. With tubular CNTs threaded into the nanoflowers, the inner electron pathways are built throughout the structure. Moreover, it is demonstrated that the CNTs adjust the MoS2 crystallinity by introducing an increased amount of S22−, which can contribute to the overall capacity during lithiation and de-lithiation reactions. The MoS2@NC@CNT, as a Li storage anode material, has an outstanding capacity of 1250 mAh g−1 at 0.2 A g−1, and reversible capacities of 947 mAh g−1 after 500 cycles of 1.0 A g−1. Furthermore, MoS2@NC@CNT shows good structural reversibility.