A self-assembled MoSe2 nanolayers/reduced graphene oxide (MoSe2/rGO) foam was prepared using a hydrothermal method. The samples were systematically investigated by X-ray diffraction, field emission scanning electron microscopy, energy dispersive X-ray spectroscopy, and high-resolution transmission electron microscopy. Electrochemical performances were evaluated in two-electrode cells versus metallic lithium. It is demonstrated that the obtained MoSe2/rGO nanocomposites show three-dimensional architecture and excellent electrochemical performance as anode materials for Li-ion batteries. The specific capacity of MoSe2/rGO anode can reach up to 650mAhg−1 at a current rate of 0.1C in the voltage range 0.01–3.0V (vs. Li/Li+), which is higher than the theoretical capacity of MoSe2 (422mAhg−1). Additionally, the fabricated half cells have shown good rate capability and long cycling stability with 10.9% capacity loss after 600 cycles under a current density of 0.5C. The excellent performance of the synthesized MoSe2/rGO is attributed to its unique nanostructure, including nanolayered MoSe2, highly conductive rGO networks and mechanically stable 3D architecture.