Different from the traditional template method, a thin amorphous carbon nanotube was prepared by constructing a polymer/SiO2 composite, utilizing the shrinking action of sulfonated polymer nanotubes (SPNTs) and the physical squeezing action of SiO2 on it during the pyrolysis of SPNT/SiO2. Remarkably, the heat treatment atmosphere (N2, N2-H2, or O2) has an important effect on the surface properties, pore structure, crystallinity, and especially the defect sites, leading to different lithium storage performances. Particularly, the sample calcined in N2-H2 (NHCNTs) exhibits outstanding reversible capacity (400.6 mA h g-1 at 2 A g-1 after 200 cycles) and rate capability (268.4 mA h g-1 at 5 A g-1 and 212.1 mA h g-1 at 10 A g-1 after 400 cycles), which are attributed to the thin-walled tubular structure and abundant defect sites. NOCNTs can be obtained by the thermal treatment of NCNTs (the sample of polymer pyrolysis in N2) in air, and the oxygen content was increased. However, the destruction of the tubular structure led to poor electrochemical properties. These results proved the importance of the thin-walled tubular structure to the electrochemical properties. Surely, this strategy for preparing thin-walled carbon nanotubes can be widely extended to the preparation of other nanomaterials with thin-walled structures.