A comparative study of the electrochemical performances of carbon nanotubes and tube-in-tube carbon nanotubes reveals a dependence effect of lithium-ion storage behavior on the detailed nanostructure of carbon nanotubes. In particular, the impurity that graphitic particles or graphene fragments inherently present in carbon nanotubes plays a crucial role in the lithium-ion storage capacity of the carbon nanotubes. Compared to acid-washed carbon nanotubes, the assembly of graphitic impurity fragments in the tube-in-tube structures hinders lithium-ion diffusion, thus drastically decreasing the rate performance of lithium-ion storage. Significantly, our results indicate that the lithium-ion storage capacity of carbon nanotubes as anode electrodes can be improved or controlled by optimizing the microstructure composition of impurity graphitic nanoparticles or graphene fragments in the matrix of the carbon nanotubes.