Silicon, as a promising electrode material for high energy density lithium ion batteries, experiences large strains and stresses during lithiation and delithation. The coupling effect between stress and lithium diffusion leads to a grand challenge to optimizing the design of Si electrodes with high capacity and high rate capability, particularly considering the amorphization of Si during initial cycles. In this study, we established a relationship between stress and the diffusion coefficients of Li in amorphous Si by ab initio molecular dynamics calculations (AIMD). The prediction from AIMD was validated by the potentiostatic intermittent titration measurements. Our results showed that two Li diffusion mechanisms can operate depending on the stress state. Specifically, the stress can increase Li diffusion either through increasing free volume under tension or by changing local structure under compression. However, within the range of stress generated during the lithiation and delithation process, diffusion coefficients are expected to vary by only one order of magnitude.