The metal-organic frameworks (MOFs) have gained considerable attention owing to their unique structures with tunable three-dimensional porous frameworks and numerous applications. The large surface area and great porosity make MOFs a promising electrode material for lithium-ion batteries. In this work, the focus is placed on an unexplored key issue, i.e., the impact of lithiation/delithiation on the structure of MOFs as anode materials. To do so, Al-MOF (chemical formula: Al(OH)[O2C–C6H4–CO2]) particles are synthesized, and then uniformly covered by graphene to form the Al-MOF/graphene composite. It is found that the lithiation/delithiation induces a pronounced structural change in the Al-MOF particles, which manifests as an order-disorder transition. This transition leads to the more open channels, thereby benefiting the diffusion and storage of Li+ ions. Compared with pure Al-MOF, the Al-MOF/graphene composite exhibits significantly enhanced electrochemical performances. Its capacity increases continuously from 60 to 400 mAh g−1 at the current density of 100 mA g−1. This work indicates that both the lithiation/delithiation induced order-disorder transition in MOFs and the optimized wrapping of MOF by graphene are crucial for enhancing the capacity and the cycling stability of anode materials.