The dual transition metals CoS2–SnO2@ reduced graphene oxide heterostructure quantum dots (shorten as CoS2–SnO2@rGO QDs) is intentionally synthesized by hydrothermal method. The compositions, grain sizes and contents of the synthesized CoS2–SnO2@rGO QDs are identified and calculated from XRD pattern. The layered structures and crystal sizes (<10 nm) of CoS2–SnO2 heterostructure quantum dots are confirmed by TEM high-resolution image. Moreover, the CoS2–SnO2@rGO QDs deliver higher specific capacity of 940.4, 781.9, 673.8, 506.6 and 303.1 mAh g−1 at 0.2, 0.5, 1.0, 2.0 and 4.0 A g−1, respectively, and remained 521.4 mAh g−1 (300 cycles) with 98.9% Coulomb efficiency under 1.0 A g−1 cycling. The DFT (density functional theory) calculation results suggest that the Li ions should diffuse through two possible paths with relatively lower Ebar values of 0.519 and 0.566 eV in CoS2–SnO2@rGO QDs. Combining with XRD, XPS, TEM and DFT calculation, we therefore assign the excellent electrochemical performances of CoS2–SnO2@rGO QDs to its highly active CoS2–SnO2 interfaces for electrode reactivity enhancement, to the characteristic heterointerfaces for “extra” Li+ ions storage/release, and to super conductive/layered rGO network for better ionic/electronic transport. The successful synthesis of CoS2–SnO2@rGO QDs may provide a strategy for dual/multi-transition metal heterojunction to enhance lithium-ion battery electrode materials.