Lithium ion batteries (LIBs) work under sophisticated external force field and its electrochemical properties could be modulated by strain. Owing to the electro-mechanical coupling, the change of micro-local-structures can greatly affect lithium (Li) diffusion rate in solid state electrolytes and electrode materials of LIBs. In this study, we find that strain gradient in bilayer graphene (BLG) significantly affects Li diffusion barrier, which is termed as the flexo-diffusion effect, through first-principles calculations. The Li diffusion barrier substantially decreases/increases under the positive/negative strain gradient, leading to the change of Li diffusion coefficient in several orders of magnitude at 300 K. Interestingly, the regulation effect of strain gradient is much more significant than that of uniform strain field, which can have a remarkable effect on the rate performance of batteries, with a considerable increase in the ionic conductivity and a slight change of the original material structure. Moreover, our ab initio molecular dynamics simulations (AIMD) show that the asymmetric distorted lattice structure provides a driving force for Li diffusion, resulting in oriented diffusion along the positive strain gradient direction. These findings could extend present LIBs technologies by introducing the novel strain gradient engineering.