The gram-scale synthesis of graphene based mesoporous SnO2 composite (G-M-SnO2) has been successfully realized based on kirkendall effect. When used as anode for lithium ion batteries, it delivers a high reversible capacity of 1354 mAhg−1 after 50 cycles at 100 mAg−1 and excellent rate capability of 664 mAhg−1 at 2 Ag−1. The outstanding lithium storage performance mainly results from the synergistic effect of the ultrasmall SnO2 and conductive graphene nanoparticles, which not only enhanced the conductivity of the whole electrode but also provide buffer matrix for the expansion of SnO2 nanoparticles during charge-discharge process. Furthermore, the ultra-small size of SnO2 shortens the diffusion length of Li+/e− in SnO2.