The Nb/Al-AlOx/Nb (SIS) Josephson junction is a crucial component in many types of superconducting devices. However, it can be easily damaged during the plasma fabrication processes. Anodic oxidation is an effective method for protecting SIS junctions by oxidizing Nb and Al from the junction profile. We used a custom wafer-scale anodic oxidation system and a neutral electrolyte to study the oxidation process of Nb films and Nb-Al(-AlOx)-Nb junctions. The oxidation process was thoroughly characterized by considering factors such as morphology and electrical properties. Anodization spectroscopy revealed varying oxidation sections from the top Nb layer to the bottom layer, extending across the Al-AlOx interlayer. This indicates that a 4 nm Al layer is sufficient to cover the surface of the bottom Nb film. High-resolution transmission electron microscopy (HRTEM) and energy dispersive spectroscopy (EDS) revealed that the Nb2O5 layer produced from the oxidation of the bottom Nb layer penetrated the Al2O3 layer and migrated to the top surface as the oxidation voltage increased. The top Nb layer of the SIS junction was also subjected to oxidation, despite the presence of a protective photoresist. Following the anodic oxidation process, the entire wafer surface was coated with an insulating Nb2O5 film. This film provided protection for the SIS junctions during the subsequent microfabrication process. The fabricated junction array, consisting of 128 junctions, demonstrated uniform electrical properties benefiting from the anodic oxidation process. This systematic analysis will further the research and practical applications of SIS junctions.