<i>Sclerotinia sclerotiorum</i> (<i>S. sclerotiorum</i>), a necrotrophic phytopathogen, causes sclerotinia stem rot (SSR) in many crops like oilseed rape, resulting in severe economic losses. Developing eco-friendly compound fungicides has become a critical research priority. This study explored the combination of sodium selenite and cuminic acid to screen for the optimal mixing ratio and investigate its inhibitory effects and mechanisms against <i>S. sclerotiorum</i>. The results demonstrated that synergistic effects were observed with a 1:3 combination ratio of sodium selenite to cuminic acid. After treatment with the selenium compound agent, ultrastructural observations revealed that the hyphae of <i>S. sclerotiorum</i> became severely shriveled, deformed, and twisted. The agent significantly reduced oxalic acid production and the activities of polymethylgalacturonide (PMG) and carboxymethylcellulose enzymes (Cx), while increasing the exocytosis of nucleic acids and proteins from the mycelium. Foliar application of the selenium compound agent significantly reduced lesion areas in rapeseed. Combined with the results of transcriptome sequencing, this study suggests that the compound agent effectively inhibits the growth of <i>S. sclerotiorum</i> by disrupting its membrane system, reducing the activity of cell wall-degrading enzymes, and suppressing protein synthesis, etc. This research provides a foundation for developing environmentally friendly and effective fungicides to control <i>S. sclerotiorum</i>.