Despite high theoretical specific capacity and uniform interlayer channel for accommodation of ions, poor cycling stability and rate capacity have been identified as critical roadblocks to further development of MoS2-based lithium ion batteries (LIBs) or sodium ion batteries (SIBs). In this study, few-atomic-layered MoS2 hollow nanospheres with expanded interlayer spacing, due to alternate intercalation of N-doped monolayer carbon (m-C) between the adjacent MoS2 monolayers, have been designed and synthesized via an annealing-followed soft-template approach. As an anode of SIBs, the ultrathin-layered m-C/MoS2 superstructures electrode can deliver a reversible discharge capacity of 401 mA h g−1 at 200 mA g−1 after 150 cycles. It can maintain 262 mA h g−1 at 2000 mA g−1 after 600 cycles with a capacity retention of 105% in comparison with that of the 2nd cycle. For LIBs, the hollow nanospheres can also deliver a reversible discharge capacity of 1025 mA h g−1 at 1000 mA g−1 after 80 cycles. The excellent electrochemical performance can be attributed to the synergy effect of expanded interlayer spacing (improving ion diffusion mobility), ultrathin feature (shortening ion diffusion paths) and alternate intercalation of monolayer carbon (improving the electrical conductivity and maintaining the structural integrity), which ensures new opportunities for designing advanced two-dimensional hosts for energy storage devices.