Exploring versatile strategies for microstructural evolution and surface modification are of fundamental importance in the development of advanced electrode materials. In this work, we report that electron-beam irradiation is a facile approach to perform surface modification for the ultrathin cross-stacked graphene aerogels loaded with SnO2 quantum dots, resulting in a remarkable modulation on the lithium storage performance. It is found that the as-synthesized SnO2/graphene aerogels composites irradiated at 280 kGy exhibit excellent high reversible lithium storage capacity, good rate capability and cycling stability, which retains a discharge capacity of 703 mAh g−1 after 50 cycles at 0.1 C rate. Microstructure analysis indicates that the enhanced electrochemical properties are mainly attributed to the exfoliation of graphene nanosheets, the increase of amorphization, disorder, defects and the removal of partial oxygen-containing functional groups on the surface of graphene nanosheets. The strategy presented here demonstrates that the electron-beam irradiation is a potential strategy to improve the electrochemical performance of graphene-based metal oxides.