Rietveld refinements were performed on synchrotron X-ray powder diffraction patterns of Li1.05Mn2O4−δ, Ni- and Ti- doped Li1.05Mn2O4−δ to investigate the structural changes in conjunction with the non-adiabatic small polaron-hopping behavior. Samples with and without substitution were confirmed to belong to the Fd3¯m space group of the cubic system. The lattice parameters a and the oxygen positional parameters u decreased with increasing Ni content, and increased with increasing Ti content. In Ni-doped samples, M−O bond lengths (M: transition metal at the 16d site) were shorter and O-M-O angles were larger than those of Li1.05Mn2O4−δ. The local distortion in MO6 octahedra decreased as a result of Ni substitution. The less distorted MO6 octahedra enhanced the overlap of the Mn 3d and O 2p wave functions. This may explain why the polaron-hopping energies WH of Li1.05Mn2−xNixO4−δ (x = 0.2 and 0.3) are smaller than that of Li1.05Mn2O4−δ. Ti substitution kept the increase of M−O bond length small. The O-M-O angle decreased slightly compared to that of Li1.05Mn2O4−δ, but barely changed with increasing Ti content. Structural changes in MO6 octahedra by Ti substitution were too small to affect the overlap of the Mn 3d and O 2p wave functions. This explains why the hopping energies WH of Li1.05Mn2−xTixO4−δ remained unchanged. Ni and Ti have different ionic radii from Mn. Thus, substitution of Ni and Ti modify the lattice distortion, and consequently induced a gradual increase in the self-trapped polaron’s energy, i.e., the activation energy of thermopower ES.