Nanostructured LiNi0.5Mn1.5O4 with two different space groups (P4332 and Fd-3m) were synthesized respectively, by using ammonia-mediated carbonate precipitation. X-ray diffraction and Rietveld refinement revealed that Li/Ni antisite defects exist in ordered as well as disordered LiNi0.5Mn1.5O4 cathode materials. Although the degree of Li/Ni antisite defects in Fd–3m space group was larger compared with that in P4332 space group, it showed better electrochemical performance. Electrochemical impedance spectroscopy confirmed that the LiNi0.5Mn1.5O4 with an Fd–3m space group has lower charge transfer resistance. Combined with differential curves, we further revealed that there is a faster phase transition during the Li+ intercalation process in the LiNi0.5Mn1.5O4 with an Fd–3m space group than in the LiNi0.5Mn1.5O4 with a P4332 space group.