Currently, constructing an advanced structure to address the weaknesses of MnO-based anode materials in regard to large volume variation upon cycling and inferior conductivity still needs to be further improved for endowing the MnO anode with a desirable lithium-storage performance. Herein, an ingenious sandwich-like CNT@MnO@N-doped carbon coating (NC) hetero-nanotube architecture with partial MnO being inlaid into CNT is synthesized through an elaborate route including template and coating strategy and utilized as a hopeful lithium-ion anode material exhibiting large specific capacity, long-term cyclability, and high rate capacity synchronously. The outer NC layer could not only enhance the electro-conductibility of MnO as well as efficiently confine the reaggregation and ameliorate the volume variation of MnO nanoparticles upon cycling, but also avert the direct contact between MnO and electrolyte which could lead to the unexpected depletion of lithium. The inner CNT could ensure the 1D hetero-nanotube structure benefiting to preserve the structural integrity during cycling, and also facilitate the electron transport. Additionally, the inlaying of MnO nanoparticles into CNT could boost the transfer and storage of lithium ion. Therefore, the CNT@MnO@NC electrode reveals a high Li+ storage capacity (665 mAh g−1 at 0.1 A g−1), outstanding cycling performance (617 mAh g−1 after 500 cycles at 1 A g−1) and superior rate capability (421 mAh g−1 at 2.0 A g−1), calculating based on the weight of CNT@MnO@NC composite. According to kinetic study, it is uncovered that the CNT@MnO@NC electrode presents an enhanced capacitive effect towards Li+ storage, featuring with the characteristic faradaic surface pseudocapacitive charge-storage mechanism. This work puts forward a promising strategy to prepare 1D heterostructured anode materials with improved conductivity and structure stability for boosting lithium-storage.