Hybrid MoS2/C nanostructures have shown great promise as an ideal anode for lithium-ion batteries (LIBs) owing to the improved conductivity and electrochemical performance. Nevertheless, if only one side of MoS2 particles is covered by conductive carbon layer, other exposed side is still low conductivity. Meanwhile, the structure of electrodes is relatively not robust. Herein, an effective structural engineering strategy has been proposed for achieving a new type of polypyrrole-derived carbon nanotubes@MoS2@carbon (PCN@MoS2@C) sandwiched architecture via a facile one-pot hydrothermal process. When utilized as anodes for lithium storage, the resulting MoS2/C hybrid exhibits a large specific capacity of 1079 mA h g−1 at 0.1 A g−1 and high coulombic efficiency of above 99.0% over 200 cycles, showing a superior cycling stability and reversibility. The density functional theory (DFT) calculations further demonstrate that ultrathin MoS2 nanosheets with an expanded interlayer distance of 0.98 nm have more accessible space, lower transfer resistance, and faster diffusion kinetics of Li ions. The great improvement in electrochemical properties is mainly ascribed to the design of peculiar hybrid architecture, and the collaborative effect between active MoS2 nanosheets and two different conductive carbon layers. This work sheds a new light on the rational design of advanced electrode materials with boosted performance and stable structural stability.