Developing anode materials for lithium-ion batteries with excellent electrochemical performance is crucial to satisfy the requirement for energy storage. Molybdenum disulfide is recognized as a prospective anode material due to its high theoretical capacity and two-dimensional layered structure. However, its further application is mainly hindered by its poor electronic conductivity. Herein, we report Mn-doped MoS2 nanosheets anchored on hierarchical carbon skeleton (MMSC) acting as an anode material. The as-synthesized electrode exhibits a high initial discharge capacity of 1280 mAh g(-1) at a current density of 0.1 A g(-1), high rate capacity (920 mAh g(-1) at 2 A g(-1)), and long-time cycling stability (71% capacity retention after 1000 cycle). Compared to that of pristine MoS2 electrode, the improved performance of MMSC anode can be attributed to the synergetic effects of optimized composite structure and Mn doping. The hierarchical carbon skeleton provides a larger surface area, allowing effective electrolyte penetration and preventing aggregation of MoS2 nanosheets in charge/discharge cycles. To further understand the mechanism of the improved rate capability, calculation of corresponding atomic models according to experimental results and first-principles calculation are conducted. The calculated results prove that the Mn-doped MoS2 (MMS) has a lower diffusion barrier of Li+ than that in pristine MoS2. Moreover, the as-synthesized MMSC electrode also demonstrates better electronic conductivity because of the electronic injection by Mn atoms.