Controllable layered MoS2 on 3D graphene aerogel (MoS2/GA) was synthesized via a facial hydrothermal process. As-prepared MoS2/graphene hybrid aerogels with desirable sizes serve directly as free-standing and binder-free anodes for lithium-ion batteries (LIB) without the need for mechanical cutting or mixing. The mechanical properties of MoS2/GA samples were quantitatively investigated to demonstrate their high mechanical robustness with Young's modulus values up to 59.2 kPa and recoverable deformability of 90% elastic strain, indicating their ability to resist large-scale deformation or fatigue stress during LIB applications. Moreover, the effects of the MoS2 mass loading on both microstructure and electrochemical performance of MoS2/GA were systematically investigated. Hierarchical nanostructures of MoS2/GA with a mass ratio of MoS2 to graphene oxide as 1:2.5 exhibit a high specific capacity of 1360.5 mAh g(-1) at a current density of 100 mAh g(-1). These materials also have desirable rate capability and good cyclic stability, demonstrating their utility in energy storage devices.