To investigate whether properties of oxygen vacancies in amorphous oxides differ from those in crystalline oxides, we examined neutral oxygen vacancies in amorphous SnO2 by first-principles and informatics approaches. We found two types of unique atomic and electronic structures of oxygen vacancies, namely, lone-pair and Sn–Sn dimer structures, in contrast to the case of crystalline SnO2. Detailed analysis revealed the correlation of the unique structures with the Bader charges of the relevant Sn atoms. Furthermore, informatics approaches indicated that a large empty space around a Sn atom and a long Sn–O bond facilitates electron localization, resulting in smaller Bader charges. These results demonstrate how by combining first-principles calculation and informatics one can analyze the relationship between diverse atomic and electronic structures like those in amorphous materials.