Sclerotinia sclerotiorum (S. sclerotiorum) is a soil-borne pathogen with broad host range. Dissolved organic matter (DOM) plays a vital role in regulating microbial activity in soil. Exogenous selenium (Se) inhibits plant pathogen growth and enhances the capacity of plants to resist disease. DOM from rape straw with Se treated in soil (FtSDOMse) was extracted, and the inhibitory effect on S. sclerotiorum growth was investigated. RSDOMSe inhibited S. sclerotiorum growth, which not only caused severe damage to S. sclerotiorum hyphae but also enhanced soluble protein leakage, thereby improving the growth inhibition ratio by 20.9%. As the action in intercellular, RSDOMSe led to a significant increase in oxalic acid and decrease in CWDE (cell wall-degrading enzyme, which helps pathogens to invade plants) activities, downregulation of Bi1 (BAX inhibitor-1, required for S. sclerotiorum virulence), Ggt1 (gamma-glutamyl transpeptidase, regulates the ROS antioxidant system), CWDE2 and CWDE10 gene expression levels, compared with non-Se treated RSDOM (RSDOMN). Eight metabolites upregulated in RSDOMSe were identified by GC-TOF-MS, and among these metabolites, fumaric acid, maleic acid, malonic acid, mucic acid, saccharic acid, succunic acid and phenylacetic acid showed significant inhibition on S. sclerotiorum growth. These findings provide valuable insight into a new approach for developing eco-friendly fungicides.