Cross-nanoflower CoS2 on rGO nanosheets has been synthesized by simply controlling the pre-reaction step during hydrothermal route. Three-dimensional CoS2 cross-nanoflowers of 150–200 nm in diameter are formed in-situ through self-assembling with rGO nanosheets reduced from GO (shorten as CoS2–NF/rGO-NS). From XRD, SEM, XPS and TEM analysis, these CoS2 nanoflowers are composed of single crystal nano-slices of 20–30 nm in thickness and evenly distributed in the networks of flexible/conductive rGO nanosheets. Owing to both capacitive-controlled and diffusion-controlled mechanisms existing in the discharging/charging processes, CoS2–NF/rGO-NS composites show excellent rate performance and cycling stability as anode materials. According to DFT calculations/simulations, the corresponding diffusion barrier (E bar) is derived to be 0.47 eV along ⟨100⟩ diffusion direction for CoS2 cross-nanoflower, indicating an effective lithium ion diffusion channel. Their enhanced electrochemical properties are therefore attributed to synergistic effects of two components: highly active/stable nanoflower-like CoS2–NF structure and flexible/conductive reduced graphene nanosheets (rGO-NS).