In this paper, we study the effect of the Jahn-Teller (JT) distortion on the Li ion migration energy barrier in spinel TiO2 by using first-principles calculations. Our results show that the JT distortion can be beneficial, harmful, and unaffected to the Li ion migration, depending on the Li ion migration pathway and the orientation of the JT distortion. Bond length analysis demonstrates that the JT distortion of the Ti3+ O-6 octahedron causes the variation of the linked Li-O bond lengths and the corresponding Li-O Coulomb energies, thus resulting in the diversity of Li ion migration barrier. In the lithiated LiTi2O4 state, the Li vacancy migration is also substantially affected by the JT distortion, while the influence of the JT distortion is much more complicated as more Ti3+ ions are created and the distribution of them is random. Our results are helpful to reveal the mechanism of Li ion migration in the spinel structures with JT distortions.