Cubic Spinel MnCo2O4/graphene sheets (MCO/GS) nanocomposites are synthesized by a facile hydrothermal method with a subsequent annealing process. Nano-sized MnCo2O4 particles are evenly embedded in paper-like graphene sheets, possessing a unique nanoparticles-on-sheets hybrid nanostructure, with particle size around 20–50 nm. Owing to the special nanoparticles-on-sheets structures, MCO/GS nanocomposites have an outstanding electrochemical performance for rechargeable energy storage devices. As an anode material for lithium-ion batteries, MCO/GS electrodes exhibit high reversible discharge capacities (1350.4 mAh g−1 at the initial rate of 100 mA g−1), excellent rate capability (462.1 mAh g−1 at a current rate of 4000 mA g−1) and outstanding cycling performance (584.3 mAh g−1 at 2000 mA g−1 after 250 cycles). Meanwhile, as an anode material for sodium-ion batteries, MCO/GS electrodes also exhibit comparably promising electrochemical characteristics. Greatly improved electrochemical properties can be assigned to the special advantageous nanostructures. Besides, the existence of graphene sheets is beneficial to the transportation of ions/electrons during battery operation. The outstanding electrochemical performance demonstrates that the lithium/sodium storage capability of MCO/GS nanocomposites is highly promising for high-capacity batteries.