Sn-based materials are one promising high-capacity anode material for lithium-ion batteries. The practical application of Sn-based materials is generally restricted by their significant capacity fading due to the volume expansion and structural changes during Sn alloying/dealloying process. In this work, Sn-SnO2 hybrid nanoclusters are embedded into carbon nanotube network, forming a Sn-SnO2@CNT composite. The Sn-SnO2 nanoclusters are consisted of interconnected Sn and SnO2 nanocrystals, in which SnO2 forms a beneficial environment for the alloying/dealloying of Sn. The ultrafine particle size of SnO2 (<10 nm) also allows a highly reversible conversion reaction, contributing to high overall capacities. The Sn-SnO2 nanoclusters are uniformly dispersed in CNT matrix, therefore providing abundant active sites for Li-ion storage. The CNT matrix functions in improving electrical conductivity, preventing Sn aggregation, and accommodating Sn volume change in prolonged cycles. As a result, the hybrid Sn-SnO2@CNT electrode shows excellent rate capability (1059 mAh g−1 at 1 A g−1 and 960 mAh g−1 at 5 A g−1, corresponding to 0.53 mAh cm−2 at 0.5 mA cm−2 and 0.48 mAh cm−2 at 2.5 mA cm−2) and outstanding cycling stability (86% capacity retention after 1000 cycles at 0.5 A g−1), making it an promising anode material for high-performance lithium-ion batteries.