Rice false smut, caused by the fungal pathogenUstilaginoidea virens, is a worldwide rice fungal disease. However, the molecular mechanism of the pathogenicity of the fungusU. virensremains unclear. To understand the molecular mechanism of pathogenesis of the fungusU. virens, we performed an integrated analysis of the transcriptome and metabolome of strongly (S) and weakly (W) virulent strains both before and after the infection of panicles. A total of 7932 differential expressed genes (DEGs) were identified using transcriptome analysis. Gene ontology (GO) and metabolic pathway enrichment analysis indicated that amino acid metabolism, autophagy-yeast, MAPK signaling pathway-yeast, and starch and sucrose metabolism were closely related to the pathogenicity ofU. virens. Genes related to pathogenicity were significantly upregulated in the strongly virulent strain, and wereATG,MAPK,STE,TPS, andNTHgenes. However, genes involved in the negative regulation of pathogenesis were significantly downregulated and contained TOR kinase,TORC1, and autophagy-related protein genes. Metabolome analysis identified 698 differentially accumulated metabolites (DAMs), including 13 categories of organic acids and derivatives, lipids and lipid-like molecules, organoheterocyclic compounds. The significantly enriched pathways of DAMs mainly included amino acids and carbohydrates, and they accumulated after infection by the S strain. To understand the relevance of DEGs and DAMs in the pathogenicity ofU. virens, transcriptomic and metabolomic data were integrated and analyzed. These results further confirmed that the pathogenesis ofU. virenswas regulated by DEGs and DAMs related to these four pathways, involving arginine and proline metabolism, lysine biosynthesis, alanine, aspartate and glutamate metabolism, and starch and sugar metabolism. Therefore, we speculate that the pathogenicity ofU. virensis closely related to the accumulation of amino acids and carbohydrates, and to the changes in the expression of related genes.