Therapy using hot springs, including the high-level radioactive gas “radon”, is traditionally conducted as an alternative treatment for various diseases. Oxidative-stress-related diseases are inhibited by the enhancement of antioxidative functions following radon inhalation. We have reported that radon inhalation increased the level of anti-oxidants, such as glutathione (G-SH), in the brain and had a protective antioxidative effect against transient global cerebral ischemic injury. However, no studies have yet revealed the changes in G-SH associated substances after radon inhalation. In this study, we comprehensively analyzed several metabolites, focusing on G-SH. Mice were exposed to radon at concentrations of 200, 2000, or 20,000 Bq/m3 for 1, 3, or 10 days. We detected 27 metabolites in the mouse brains. The result showed that the L-methionine levels increased, whereas the levels of urea, glutathione, and sulfite ion decreased under any condition. Although the ratio of G-SH to oxidized glutathione (GS-SG) decreased, glutathione monosulfide (G-S-SH) and cysteine monosulfide (Cys-S-SH) increased after radon inhalation. G-S-SH and Cys-S-SH can produce a biological defense against the imbalance of the redox state at very low-dose irradiation following radon inhalation because they are strong scavengers of reactive oxygen species. Additionally, we performed an overall assessment of high-dimensional data and showed some specific characteristics. We showed the changes in metabolites after radon inhalation using partial least squares-discriminant analysis and self-organizing maps. The results showed the health effects of radon, especially the state of sulfur-related metabolites in mouse brains under the exposure conditions for radon therapy.