A novel Graphdiyne-Molybdenum disulfide (GDY-MoS2) hybrid nanostructure is successfully synthesized through in-situ method. The compactly contact through carbon-sulfur (C-S) bond between graphdiyne (GDY) and molybdenum disulfide (MoS2) effectively prevents the detachment problem and also provides effective electron transport paths between them. Highly conductive GDY layer not only acts as an electron collector, but also provides the volume expansion space for MoS2. And the large contact surface area of GDY and MoS2 can exceedingly shorten the diffusion distance of lithium-ion. As the synergistic results of the distinct hybrid structure, highly conductive GDY layer, as well as the robust interconnection, GDY-MoS2 (with 77.9 wt% MoS2) exhibits excellent lithium-ion storage performance (1463 mAh g(-1) at 0.05 A g(-1)) and super cycling stability when serving as lithium-ion batteries (LIBs) anode.