Molybdenum disulfide (MoS2), which possesses a layered structure and exhibits a high theoretical capacity, is currently under intensive research as an anode candidate for next generation of Li‐ion batteries. However, unmodified MoS2 suffers from a poor cycling stability and an inferior rate capability upon charge/discharge processes. Herein, a unique nanocomposite comprising MoS2 nanothorns epitaxially grown on the backbone of carbon nanotubes (CNTs) and coated by a layer of amorphous carbon is synthesized via a simple method. The epitaxial growth of MoS2 on CNTs results in a strong chemical coupling between active nanothorns and carbon substrate via CS bond, providing a high stability as well as a high‐efficiency electron‐conduction/ion‐transportation system on cycling. The outer carbon layer can well‐accommodate the structural strain in the electrode upon lithium‐ion insertion/extraction. When employed as an anode for lithium storage, the prepared material exhibits remarkable electrochemical properties with a high specific capacity of 982 mA h g−1 at 0.1 A g−1, as well as excellent long‐cycling stability (905 mA h g−1 at 1 A g−1 after 500 cycles) and superior rate capability, confirming its potential application in high‐performance Li‐ion batteries.