X-ray induced photodarkening and its suppression by Ge-codoping were investigated in Al-doped, Dy-doped, and Dy-Al-doped silica glasses. Absorption bands of 4f-4f5d transition of Dy2+ were determined in Dy-Al-doped silica glass fabricated by Si nano-powders as a reducing agent, and it was found that pair generation of Dy2+ and Al-OHC was occurred in X-ray irradiated Dy-Al-doped silica glass. Ge-codoping suppresses the above-mentioned pair generation and instead forms the pair of GEC and GLPC+. Similar suppression effect of Ge-codoping was observed in Al-Ge-doped silica glass, where pair generation of Al-OHC and Al-E’ center was suppressed. To investigate the stability of defects, annihilation processes during thermal annealing was measured. Al-OHC and Dy2 + are destabilized by Ge-codoping in Al-doped and Dy-Al-doped silica glasses, while GEC is stabilized in Al-Ge-doped and Dy-Al-Ge-doped silica glasses. Based on these results, local structure models around Al, Ge, and Dy ions and possible mechanisms of photodarkening were proposed