The powdered crystalline samples of nominal composition Li1.07Mn1.93O4-δ have been investigated by transmission electron microscopy (TEM) combined with X-ray powder diffraction (XRD) at room temperature. As suggested by the TEM observation, the dominant phase of the particles is a cubic spinel Li1+αMn2-αO4-δ with space group Fd3̅m. A monoclinic Li2MnO3 phase with C2/m space group was also identified. Furthermore, the occurrence of nanoscale rotational twinning domains in Li2MnO3 with 120° rotation angles, stacked along the [103]m/[111]c ("m" and "c" represent the monoclinic and cubic descriptions, respectively) axis was also observed. These nanoscale rotational twining domains are responsible for the pseudo-3-fold axis and their formation is supported by the superstructure reflections in selected-area electron-diffraction (SAED) patterns. Similar patterns were reported in the literature but may have been misinterpreted without the consideration of such domains. Consistent with the TEM observation, the XRD results reveal the increasing percentage of monoclinic Li2MnO3 with increasing annealing time, associated with more oxygen vacancies. In addition, the electron beam irradiation during TEM studies may cause the nucleation of nanoscale cubic spinel Li-Mn-O crystallites on the monoclinic Li2MnO3 grains. These results provide the detailed structural information about the Li1.07Mn1.93O4-δ samples and advance the understanding of corresponding electrochemical properties of this material as well as other layer structured cathode materials for lithium-ion batteries.