In this report, we present the synthesis of yolk-shell Co3O4@CuO microspheres followed with the surface modification of carboxyl-functionalized graphene quantum dots (donated as Co3O4@CuO@GQDs) and investigate their lithium storage properties. Derived from metal-organic frameworks (MOFs), the obtained yolk-shell Co3O4@CuO microspheres exhibit well-defined microstructure and high porosities. The yolk-shell Co3O4@CuO structure is designed to adapt the stepwise lithium insertion mechanism (first in CuO shell and then in Co3O4 core). In addition, the GQDs decorated on the surface of Co3O4@CuO microspheres not only provides larger specific surface area, more active sites and enhanced electronic conductivity, but also works as a buffer to alleviate the volume expansion and a reservoir for electrolyte molecules to improve the ionic conductivity. Furthermore, the -COOH groups from GQDs exhibits good hydrophilicity which is supposed to be useful for the combination of GQDs with Co3O4@CuO and also shows strong affinity to Li+. Based on the above merits from the structural and compositional design, the Co3O4@CuO@GQDs anode displays enhanced cyclability and superior lithium storage performance. Specifically, compared to the bald Co3O4@CuO microspheres without GQDs which suffer from a severe capacity decline with an inferior capacity of 414 mAh g(-1) after 200 cycles, the Co3O4@CuO@GQDs anode displays an initial specific capacity of 816 mAh g(-1) and a high reversible charge capacity of 1054 mAh g(-1) after 200 cycles at 0.1 A g(-1).