In this work, we adopt first-principle calculations based on density functional theory and Kinetic Monte Carlo simulations to investigate the adsorption and diffusion of lithium in bilayer graphene (BLG) as anodes in lithium-ion batteries. Based on energy barriers directly obtained from first-principle calculations for single-Li and two-Li intercalated BLG, a new equation was deduced for predicting energy barriers considering Lis interactions for multi-Li intercalated BLG. Our calculated results indicate that Li energetically prefers to intercalate within rather than adsorb outside the bilayer graphene. Additionally, lithium exists in cationic state in the bilayer graphene. More excitingly, ultrafast Li diffusion coefficient, within AB-stacked BLG near room temperature was obtained, which reproduces the ultrafast Li diffusion coefficient measured in recent experiment. However, ultrafast Li diffusion was not found within AA-stacked BLG near room temperature. The analyses of potential distribution indicate that the stacking structure of BLG greatly affects its height of potential well within BLG, which directly leads to the large difference in Li diffusion. Furthermore, it is found that both the interaction among Li ions and the stacking, structure cause Li diffusion within AB-stacked BLG to exhibit directional preference. Finally, the temperature dependence of Li diffusion is described by the Arrhenius law. These findings suggest that the stacking structure of BLG has an important influence on Li diffusion within BLG, and changing the stacking structure of BLG is one possible way to greatly improve Li diffusion rate within BLG. At last, it is suggested that AB-stacked BLG can be an excellent candidate for anode material in Lithium-ion batteries.