To overcome the disadvantages of the MoS2 anode for LIBs in terms of low intrinsic conductivity, poor mechanical stability, and adverse reaction with electrolytes, a 3D multilevel heterostructure (VANS-MoS2-CNTs) has been successfully prepared by a simple hydrothermal method followed by thermal treatment. VANS-MoS2-CNTs are made up of 2D vertically aligned MoS2 nanosheets (VANS) and 1D sandwich C-MoS2-C nanotubes (CNTs). The sandwich-like nanotube is the core part, which is made up of the MoS2 nanotube covered by carbon layers on both side surfaces. Due to the special heterostructure, VANS-MoS2-CNTs have good conductivity, high structured stability, and excellent Li+/electron transport, resulting in high discharge capacity (1587 mAh/g at a current density of 0.1 A/g), excellent rate capacity (1330 and 730 mAh/g at current densities of 0.1 and 2 A/g, respectively), and good cyclic stability (1270 mAh/g at 0.1 A/g after 100 cycles).