Two-dimensional layered materials such as molybdenum disulfide (MoS2) have attracted great scientific interests as a promising anode material candidate for lithium-ion batteries. However, MoS2 nanosheets, the most commonly investigated structure, easily tend to restack or aggregate and also present intrinsic poor electric conductivity, which limit their applications. Herein, we highlight a rational design of the three-dimensional (3D) MoS2 hierarchitecture with tunable nanosheets and 2H/1T hybrid phase due to the confinement effect of graphene. By changing the amount of graphene in the reaction, we obtain the optimized 3D hierarchical architectures constructed from inter-crossed 2D nanosheets, which not only possess good robustness to avoid aggregation through 3D assembly but also provide large surface area and short lithium-ion diffusion via exposed 2D building blocks. In addition, it is found that the MoS2 nanosheets exhibit both 2H and 1T hybrid phase, therefore providing a fast electron pathway due to the good contacts between graphene and 1T phase. When tested as anode in lithium-ion batteries, graphene-wrapped 3D MoS2 hierarchitectures exhibit high reversible capacity of 715mAhg−1 after 50 cycles at a high current density of 2Ag−1.