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 MoO₃ and 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.