The atomic structure of a spinel-type MgCo2O4 nanoparticle was investigated by the reverse Monte Carlo modelling using X-ray and neutron total scattering data. It is found that Mg at an octahedral site induces a significant structural distortion, while Mg at a tetrahedral site is considered to move easily to a vacant site. Based on the results, we propose a guideline for the development of a better positive electrode material for a Mg rechargeable battery.