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The lithium ion dynamics in graphite, an important anode material for lithium ion batteries, is strongly related with the layer-to-layer distance (d-spacing) and the stacking modes of graphite. We studied these relationships by first-principles calculations. It is found that a larger d-spacing results in the easier transformation of the stacking mode from A-B stacking to A-A stacking when lithium atoms are inserted. This transformation is unfavorable to the lithium diffusion because of the larger diffusion energy barrier for lithium in A-A stacking graphite compared to that in A-B one. On the other hand, as the d-spacing increases, the diffusion energy barrier for lithium in A-A stacking graphite decreases substantially, thus being favorable to the lithium diffusion. These results give a better understanding of the lithium ion dynamics in graphite, and show that it is possible to optimize the lithium ion dynamics in graphite by properly adjusting the d-spacing. [ABSTRACT FROM AUTHOR]