Construction of metal oxide nanoparticles as anodes is of special interest for next-generation lithium-ion batteries. The main challenge lies in their rapid capacity fading caused by the structural degradation and instability of solid-electrolyte interphase (SEI) layer during charge/discharge process. Herein, we address these problems by constructing a novel-structured SnO2-based anode. The novel structure consists of mesoporous clusters of SnO2 quantum dots (SnO2 QDs), which are wrapped with reduced graphene oxide (RGO) sheets. The mesopores inside the clusters provide enough room for the expansion and contraction of SnO2 QDs during charge/discharge process while the integral structure of the clusters can be maintained. The wrapping RGO sheets act as electrolyte barrier and conductive reinforcement. When used as an anode, the resultant composite (MQDC-SnO2/RGO) shows an extremely high reversible capacity of 924 mAh g−1 after 200 cycles at 100 mA g−1, superior capacity retention (96%), and outstanding rate performance (505 mAh g−1 after 1000 cycles at 1000 mA g−1). Importantly, the materials can be easily scaled up under mild conditions. Our findings pave a new way for the development of metal oxide towards enhanced lithium storage performance.