Sclerotinia sclerotiorum (Lib.) de Bary is a crop-threatening fungus. Natural products are ideal antimicrobial agents to combat pathogens. They are considered a promising alternative to traditional synthetic fungicides due to low residual toxicity and possibly different modes of action on organisms. This work aims to develop a leading compound from natural products. Here, the antifungal activity of ten pentacyclic triterpenoids, including celastrol, pristimerin, asiatic acid, maslinic acid, ursolic acid, oleanic acid, quillaic acid, glycyrrhetinic acid, madecassic acid and corosolic acid were evaluated. Pristimerin exhibited an excellent activity against Sclerotinia sclerotiorum (S. sclerotiorum) with an EC50 value of 1.36 µg/mL. Subsequently, the mode of action of pristimerin on S. sclerotiorum was further characterized by RNA-Seq-Based transcriptome profile. Pristimerin mainly inhibited oxidative phosphorylation, citrate cycle (TCA cycle) and blocked energy metabolism, and it also promoted the accumulation of ROS and disrupted the balance of the active oxygen metabolism system by affecting the activities of peroxidase (POD), catalase (CAT), superoxide dismutase (SOD) in the mycelial cells, and ultimately led to cell death. And beyond that, mitochondrial damage and changes in mycelial cells were also observed by transmission electron microscope (TEM) and scanning electron microscope (SEM). In general, these findings showed a molecular level perspective on the antifungal mechanism of pristimerin against S. sclerotiorum, and it could be used as a potential fungicide against S. sclerotiorum.