Lithium-rich oxygen non-stoichiometric Li1.07Mn1.93O4−δ oxides with different oxygen vacancy values δ have been studied intensively using transmission electron microscope (TEM) at room temperature. The TEM observation shows that the dominant part of a given sample is the cubic spinel phase with secondary tetragonal phases, which have different lattice parameters. The detailed TEM study shows that the distortion level c p/a p ratio (a p and c p are the pseudo cubic unit cell parameters of the tetragonal phase) of the tetragonal phases ranges from 1.00 to 1.16. The diversity in values for the tetragonal phases is believed to be due to the differences in oxygen vacancy value among particles after annealing, which is related to the differences in their initial physical characteristics. The presence of twinning and defects in the tetragonal phases is common and the statistical results for the sample Li1.07Mn1.93O4−0.167 are given. The electrochemical test shows that the electrochemical performance of the annealed samples is dramatically deteriorated with increasing amount of oxygen vacancy.