A novel kind of plum-pudding like mesoporous SiO2 nanospheres (MSNs) and flake graphite (FG) nanocomposite (pp-MSNs/FG) was designed and fabricated via a facile and cost-effective hydrothermal method. Transmission electron microscopy (TEM) analysis showed that most of the MSNs were well anchored on FG. This special architecture has multiple advantages, including FG that offers a conductive framework and hinders the volume expansion effect. Moreover, the porous structure of MSNs could provide more available lithium storage sites and extra free space to accommodate the mechanical strain caused by the volume change during the repeated reversible reaction between Li(+) and active materials. Due to the synergetic effects of its unique plum-pudding structure, the obtained pp-MSNs/FG nanocomposite exhibited a decent reversible capacity of 702 mA h g(-1) (based on the weight of MSNs in the electrode material) after 100 cycles with high Coulombic efficiency above 99% under 100 mA g(-1) and a charge capacity of 239.6 mA h g(-1) could be obtained even under 5000 mA g(-1). Their high rate performance is among the best-reported performances of SiO2-based anode materials.