An amorphous mixing layer (3.5–4.0 nm in thickness) containing silicon (Si), oxygen (O), molybdenum (Mo) atoms, named α-SiO _x(Mo), is usually formed by evaporating molybdenum trioxide (MoO ₃) powder on an n-type Si substrate. In order to investigate the process of adsorption, diffusion and nucleation of MoO ₃in the evaporation process and ascertain the formation mechanism of α-SiO _x(Mo) on a atomic scale, the first principle calculation is used and all the results are obtained by using the Vienna ab initiosimulation package. The possible adsorption model of MoO ₃on the Si (100) and the defect formation energy for substitutional defects and vacancy defects in α-SiO ₂and α-MoO ₃are calculated by the density functional theory. The results show that an amorphous layer is formed between MoO ₃film and Si (100) substrate according to ab initiomolecular dynamics at 1500 K, which are in good agreement with experimental observations. The O and Mo atoms diffuse into Si substrate and form the bonds of Si—O or Si—O—Mo, and finally, form an α-SiO _x(Mo) layer. The adsorption site of MoO ₃on the reconstructed Si (100) surface, where the two oxygen atoms of MoO ₃bond with two silicon atoms of Si (100) surface, is the most stable and the adsorption energy is －5.36 eV, accompanied by the electrons transport from Si to O. After the adsorption of MoO ₃on the Si substrate, the structure of MoO ₃is changed. Two Mo—O bond lengths of MoO ₃are 1.95 Å and 1.94 Å, respectively, elongated by 0.22 Å and 0.21 Å compared with the those before the adsorption of MoO ₃on Si substrate, while the last bond length of MoO ₃is little changed. The defect formation energy value of neutral oxygen vacancy in α-SiO ₂is 5.11 eV and the defect formation energy values of neutral oxygen vacancy in α-MoO ₃are 0.96 eV, 1.96 eV and 3.19 eV, respectively. So it is easier to form oxygen vacancy in MoO ₃than in SiO ₂, which implies that the oxygen atoms will migrate from MoO ₃to SiO ₂and forms a 3.5–4.0-nm-thick α-SiO _x(Mo) layer. As for the substitutional defects in MoO ₃and SiO ₂, Mo substitutional defects are most likely to form in SiO ₂in a large range of Mo chemical potential. So based on our obtained results, the forming process of the amorphous mixing layer may be as follows: the O atoms from MoO ₃bond with Si atoms first and form the SiO _x. Then, part of Mo atoms are likely to replace Si atoms in SiO _x. Finally, the ultra-thin buffer layer containing Si, O, Mo atoms is formed at the interface of MoO ₃/Si. This work simulates the reaction of MoO ₃/Si interface and makes clear the interfacial geometry. It is good for us to further understand the process of adsorption and diffusion of atoms during evaporating, and it also provides a theoretical explanation for the experimental phenomenon and conduces to obtaining better interface passivation and high conversion efficiency of solar cell.