The magnetic properties of spinel nanoparticles are determined by crystal chemistry issues such as cation distribution and oxidation states. The cation distribution and oxidation state of Mn-Fe spinel nanoparticles have been systematically studied at various temperatures by using neutron diffraction and electron energy loss spectroscopy, respectively. The Mn-Fe spinel nanoparticles prepared by coprecipitation have a high degree of inversion with 61% of the tetrahedral sites occupied by Fe3+ cations. The degree of inversion correlates with the distribution expected from random occupancy of cations consisting of Fe (60%) and Mn (40%). After heat treatment in a vacuum, the cation distribution reaches an equilibrium state with a 29% inversion. Initially. one-half of the Mn cations are in the +3 oxidation state and the other half are in the +2 oxidation state. Mn3+ cations are slowly and irreversibly reduced to Mn2+ with increasing temperature. When the temperature approaches 600 degrees C, all Mn cations are in the +2 state. These results provide direct evidence for the temperature-dependent change of crystal chemistry in Mn-Fe spinel nanoparticles, which has been closely related with the controversy on attributing the changes in the magnetic properties of the nanoparticles to crystallite size effect. These results will also provide an understanding of how to control crystal chemistry in order to control the properties of these magnetic nanoparticles.