SnO2 has been widely studied in lithium-ion batteries (LIBs) because of its high theoretical specific capacity and reversible alloying reaction. Herein, we reported a novel strategy of confinement growth to implant nano-sized SnO2 crystals into N-doped hollow mesoporous carbon spheres (NHMCS) to form SnO2@NHMCS composite with unique nanoscale voids. The nanocrystals (similar to 5 nm) decrease the required activation energy for redox reactions, and the carbon shell of NHMCS improves the conductivity and structural stability. It is worth noting that this method can effectively control the filling degree of ultrasmall nanocrystals in NHMCS and adjust the nanosize of voids between nanocrystals and NHMCS. When SnO2@NHMCS is evaluated as an anode material for LIBs, it is proved to exhibit high reversible capacity and stable cycling performance, which is attributted to the appropriate content of active components and the ample buffer space for conversion reaction of SnO2 and alloying reaction of Sn. It also shows excellent electrochemical property as anode material for sodium-ion batteries.