Background: Rice false smut (RFS), caused by Ustilaginoidea virens, is widely distributed in major rice-producing regions. Previous studies showed that treating RFS with chelerythrine can decrease fungus spore germination by 86.7% and induce fungal cell apoptosis. Result: In the present study, the effects of chelerythrine on the metabolism of U. virens were explored using metabolomics, and analysing differentially expressed genes and altered metabolic pathways. A total of 1153 features (740 in positive ion mode, 401 upregulated, 339 downregulated; 413 in negative ionisation mode, 190 upregulated, 223 downregulated). The top 15 metabolites in Random Forest analysis were significantly different between groups. In positive ion mode, purine metabolism (map00230), phenylalanine metabolism (map00360), phenylalanine, tyrosine and tryptophan biosynthesis (map00400), pyrimidine metabolism (map00240) and nitrogen metabolism (map00910) were dominant. Alanine, aspartate and glutamate metabolism (map00250) and phenylalanine metabolism (map00360) were enriched in negative ion mode. Conclusion: Differentially expressed genes and altered metabolic pathways of U. virens were effected by chelerythrine. The findings support future research on the prevention and treatment of RFS by chelerythrine, and provide a theoretical basis for targeted drug delivery.