SnO2-based nanostructures have attracted considerable interest as a promising high-capacity anode materials for lithium ion batteries. We present herein a facile one step hydrothermal approach for in situ growth of SnO2 nanoparticles in heteroatoms doped cross-linked carbon framework (NSG/CNTs@SnO2). Thiourea is employed as a single source of nitrogen and sulfur in the cross-linked carbon framework (NSG/CNTs). Characterization shows that the SnO2 nanoparticles with an average size of 6–10nm are uniformly anchored on NSG/CNTs matrix. When evaluated for the electrochemical properties in lithium ion batteries, the obtained NSG/CNTs@SnO2 composite with ultrasmall SnO2 particle size (6–10nm) delivers a high reversible capacity of 999mAhg−1 at 200mAg−1 after 120 cycles and excellent rate performance. Such outstanding electrochemical performance of the peculiar cross-linked NSG/CNTs@SnO2 composite can be primarily attributed to the synergistic effect of the ultrasmall anchored SnO2 nanoparticles and the dual-doped NSG/CNTs matrix. The uniformly distributed SnO2 nanoparticles can deliver large capacity and the robust dual-doped NSG/CNTs matrix can guarantee the good structural integrity and high electrical conductivity during cycling. Besides, the porous structure can provide free space for the volume expansion of SnO2 and accommodate the strain formed during repeated lithiation/delithiation processes.