In this paper, an effective strategy to fabricate mesoporous MoS2(1-x)Se2x composites supported on graphene sheets (meso-MoS2(1-x)Se2x/rGO) for use as anode materials for lithium ion batteries (LIBs) is reported. The meso-MoS2(1-x)Se2x/rGO composites possess a two-dimensional (2D) layered structure with well-defined mesoporosity and the MoS2(1-x)Se2x nanoparticles are perpendicularly grown on graphene sheets. Due to the merits of 2D layered structural configuration and sulfur-selenium coupled effect, the meso-MoS2(1-x)Se2x/rGO composites promise the enhanced electrochemical performance for LIBs. Introduction of Se may widen the spacing of the (002) crystal plane, as a result, rendering them more effective diffusion path for both Li+ and e− during the charge and discharge process. More importantly, Se incorporation may further induce the transition of meso-MoS2(1-x)Se2x from 2H phase to more metallic 1 T phase. As such, the meso-MoS1.12Se0.88/rGO electrodes exhibit efficient rate capability and good cycling stability with an optimum capacity of 830 mA h g−1 at a current density of 100 mA g−1 for 150th cycle. The meso-MoS1.12Se0.88/rGO electrode still keeps a capacity of 415.3 mA h g−1 even when the current density is 1000 mA g−1 making them promising for potential practical application. The novel synthetic strategy may be applicable to fabricate a large variety of 2D layered chalcogenide electrode materials for LIBs.