The garnet-type lithium ion conductor, nominal Li7La3Zr2O12 (LLZO) has received a lot of interest as they are considered usable as solid electrolytes in lithium battery. The Li+ migration bottleneck size of garnet-type Li7La3Zr2O12 (LLZO) solid electrolyte are posed significant effect on Li+ transportation property. However, the regulation mechanism of the bottleneck size on the Li+ migration activation energy is not clear. In the study, equivalent substitution of tetravalent M4+ (M4+ = Ge4+, Ti4+, Sn4+, Hf4+ and Te4+) ions on Zr site of Li7La3M0.25Zr1.75O12 is designed to regulate the bottleneck size. X-ray absorption fine structure (XAFS) is applied to detect the quantitative structural information of M-doped LLZO. Experimental and calculations results show that the M4+ substitution regulate the Li+ migration bottleneck size via changing M–O bond length. The M–O bond length increases with the increase of M4+ doping ion radius which results in the increase of the bottleneck size. However, larger bottleneck size is not necessarily favorable for Li+ migration. Ge4+ and Ti4+ doped LLZO have smaller bottleneck size than the un-doped LLZO, which is more suitable for Li+ migration (corresponds to lower Ea of 0.28 eV, 0.29 eV, respectively). This study is of great significance for obtaining optimum lithium ion migration channel size for LLZO, and the regulation mechanism is universality for crystal ion conductors.