A new nanocomposite based on three-dimensional ordered mesoporous carbon (OMC) with tubular framework supported SnO2 nanoparticles entangled in MoS2 nanosheets is developed ingeniously by nanocasting and hydrothermal methods. The bimodal mesoporous interconnected architecture of CMK-9 and MoS2 nanosheets host SnO2 nanoparticles inside the mesopores and interlayer regions. Herein, for the first time, electrochemical performances of SnO2/MoS2 heterojunction are explored with an OMC. The present architecture improves the diffusion of ions and conduction of charges, which assist in achieving outstanding capacity, superior rate capability and stable cycle life when the nanocomposite is employed as the anode for lithium-ion batteries (LIBs). Among the nanocomposites, the SnO2/MoS2(1:3)@CMK-9 anode delivers a large initial discharge capacity of 2211 mA h g−1 and an outstanding discharge capacity of 1245 mA h g−1 after 300 cycles with a capacity retention of 96% as compared to the 3rd cycle (1291 mA h g−1) at a current density of 100 mA g−1. At a current density of 1000 mA g−1, the anode provides an exceptional discharge capacity of 823 mA h g−1 after 1000 cycles with capacity retention of 91% as compared to the 3rd cycle. The present architecture of SnO2/MoS2(1:3)@CMK-9 nanocomposite anode with excellent electrochemical performances signifies its potential use in next generation LIBs.