© 2018 The Author(s). We report quantitative characterization of the high temperature oxidation process by using electron tomography and energy-dispersive X-ray spectroscopy. As a proof of principle, we performed 3D imaging of the oxidation layer of a model system (Mo3Si) at nanoscale resolution with elemental specificity and probed the oxidation kinetics as a function of the oxidation time and the elevated temperature. Our tomographic reconstructions provide detailed 3D structural information of the surface oxidation layer of the Mo3Si system, revealing the evolution of oxidation behavior of Mo3Si from early stage to mature stage. Based on the relative rate of oxidation of Mo3Si, the volatilization rate of MoO3and reactive molecular dynamics simulations, we propose a model to explain the mechanism of the formation of the porous silica structure during the oxidation process of Mo3Si. We expect that this 3D quantitative characterization method can be applied to other material systems to probe their structure-property relationships in different environments.