Amorphous insulating oxides play a significant role in contemporary electronic industry. Understanding the band alignment of heterogeneous interfaces containing amorphous structures helps to better control the carrier transport property at the interface. Classical band offset methods developed in the literature align eigenlevels with respect to an ideal bulk reference or vacuum level. However, the local disorder of amorphous structures makes the bulk reference impossible to set up, which makes the classical methods inapplicable. In this study, we introduce a new approach based on the Linear Combination of Atomic Orbital (LCAO) projection of wave-function to line-up bands at metal/oxide interfaces. The LCAO projection of wave-function reveals all metal/oxide interface effects, such as built-in voltage, interface dipole, virtual oxide thinning, barrier deformation, and band bending. Therefore, it provides a complete and accurate band alignment between two different materials with different crystal structures. The method is first validated at Al/crystal-SiO2 (Al/c-SiO2) interface against experimental data and then extended to Al/amorphous-SiO2 (Al/a-SiO2) interface. For both systems (Al/c-SiO2 and Al/a-SiO2), we also observed a space charge region at the interface, which leads to non-linear band deformation in the oxide. The space charge region effectively decreases the oxide layer thickness, hence lowering its dielectric strength. This analysis is further supported by extracting hopping integrals from Maximally Localized Wannier Functions (MLWFs) across the interface. In both cases, the largest hopping integral is between two centers localized on the metal side and the oxide side. Such a hopping integral indicates the electron path across the interface that could trigger the dielectric breakdown. The hopping integral is larger for the Al/c-SiO2 than for the Al/a-SiO2. Consequently, the Al/a-SiO2 appears to be more resistant to breakdown.