3D hierarchical SnS2 microspheres have been designed and fabricated via a one-pot biomolecule-assisted hydrothermal method. When used as anode material in rechargeable Li-ion batteries, the as-formed SnS2 microspheres self-assembled by layered nanosheets, show high lithium storage capacity, long-term cycling stability and superior rate capability. After charge–discharge for 100 cycles, the remaining discharge capacities are kept as high as 570.3, 486.2, and 264mAhg−1 at 1C (0.65Ag−1), 5C, and 10C rate, respectively. Such outstanding performance of these SnS2 microspheres is ascribed to their unique 3D hierarchical structures. The new charge–discharge mechanism of 3D SnS2 microsphere as anode in Li-ion battery is further revealed.