<p>Silicon (Si) has been demonstrated to enhance oat resistance to stem rust, caused by <i>Puccinia graminis f. sp. avenae</i> (<i>Pga</i>). However, the molecular mechanisms underlying Si-mediated resistance against <i>Pga</i> remain poorly characterized. To address this, we performed transcriptomic and metabolomic analyses on oat plants treated with or without Si and inoculated with <i>Pga</i>. Our results showed that Si treatment increased the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) under <i>Pga</i> infection, thereby inhibiting reactive oxygen species (ROS) accumulation. Transcriptomic analysis identified 143 differentially expressed genes (55 upregulated, 88 downregulated) in Si-treated plants. Most of these genes were associated with diterpenoid biosynthesis, zeatin biosynthesis, and phenylpropanoid biosynthesis. Metabolomic profiling revealed 69 significantly enriched metabolites, including carbohydrates, organic acids, amino acids, and secondary metabolites. Based on KEGG database annotation, these metabolites were primarily involved in arginine biosynthesis; alanine, aspartate, and glutamate metabolism; cyanoamino acid metabolism; aminoacyl-tRNA biosynthesis; pyrimidine metabolism; and purine metabolism. Integrative analysis of transcriptome and metabolome data indicated that Si treatment significantly altered key metabolic pathways in oat leaves, including tryptophan metabolism, glyoxylate and dicarboxylate metabolism, porphyrin metabolism, and chlorophyll metabolism. Collectively, these findings provide novel molecular insights into Si-mediated enhancement of oat resistance to stem rust.</p>