Two kinds of hollow mesoporous carbon nanospheres (HMCNs) are synthesized by molecular self-assembly in solution, carbonization and followed etching technique with different silicon precursors “tetraethyl orthosilicate (TEOS, labeled as E) and tetrapropyl orthosilicate (TPOS, labeled as P)”. The growth and Na+ storage mechanisms of HMCNs are proposed via systematically structural characterization and electrochemical analysis. Both two kinds of HMCNs deliver satisfactory Na+ storage performance when used as anode materials for sodium-ion batteries (SIBs), in which HMCNs-E exhibits higher specific capacity (386.5 mAh g−1 at 100 mA g−1 for initially reversible discharge and 207.7 mAh g−1 after 100 cycles) and better rate capability (152.5 mAh g−1 even under 1 A g−1 after 1000 cycles). This could be attributed to the smaller pore size and thinner shell of HMCNs-E compared to HMCNs-P, which not only allows the sufficient approach of Na+ center to electrode surface, but provides shorter diffusion length and makes full use of the active sites within mesoporous shell of HMCNs-E, resulting in its better electrochemical performance.