In this study, we demonstrate a facile method to fabricate a flexible alloyed copper/silicon core-shell nanoflowers structure anchored on the three-dimensional graphene foam as a current collector. This combination provides flexible and free-standing structure and three-dimensional conductive network, allowing unique properties for current collection and transmission. The copper oxide nanoflowers are synthesized on the three-dimensional graphene foam by a simple electrodeposition and etching, which serves as an outstanding template to retard the stress effects during the lithiation/delithiation of silicon. After the silicon coating uniformly deposited on the copper oxide nanoflowers, a simple hydrogen annealing was applied to reduce copper oxide nanoflowers and form the copper/silicon alloy, remarkably enhancing the conductivity of silicon. Moreover, this structure can be directly assembled without any conductive additive or binder. In electrochemical testing, the resulting copper/silicon core-shell nanoflowered electrode demonstrates a high initial capacity of 1869 mAh g−1 at 1.6 A g−1, with a high retention rate of 66.6% after 500 cycles. More importantly, at a high current density of 10 A g−1, this anode still remains a high capacity retention >63% (compared with the highest capacity 679 mAh g−1), offering enormous potential for energy storage applications.