Objective::To observe the effect of Ganoderma polysaccharides (GP) on endogenous substance metabolism in radiation-injured mice by metabolomics, so as to find potential biomarkers and analyze their metabolic pathways, and to explore its mechanism of action. Method::Thirty mice were randomly divided into normal group (normal saline), model group (normal saline) and GP group (dose of 96 mg·kg^-1) for 14 days of continuous intragastric administration, 10 mice in each group, 2 h after the intragastric administration on the 7^th day, mice in the model group and GP group were subjected to whole body irradiation by X-rays, except the normal group. UPLC-Q-TOF-MS was used to detect endogenous small molecule metabolites in thymus tissue of mice. Principal component analysis (PCA)and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to compare the changes of endogenous small molecule metabolites in thees three groups, these differential metabolites among the three groups were analyzed by Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathway method. Result::A total of 34 potential biomarkers were identified, compared with the model group, it was found that the GP group had a significant reversal trend on L-glutamic acid, taurine, phosphatidylcholine (PC) and lysophosphatidylcholine (LysoPC), etc. They were involved in taurine and hypotaurine metabolism, D-glutamine and D-glutamate metabolism, glycerophospholipid metabolism. Conclusion::GP can play a role in radiation protection by improving the expression of related potential biomarkers and related metabolic pathways in thymus of radiation-injured mice.