Diseases caused by fungi can affect the quality and yield of the leaves of tea plants [Camellia sinensis (L.) Kuntze]. At present, the availability of highly effective and safe fungicides for controlling tea plants remains limited. The objectives of this study were to identify novel compounds with anti-fungal activities and to determine their molecular mechanisms. A series of sulfone compounds containing 1,3,4-oxadiazole were evaluated in China for their anti-fungal activities against several pathogens causing foliar diseases and high production losses. Transcriptomics and bioinformatics were used to analyze the differentially expressed genes of Lasiodiplodia theobromae treated with a representative compound, Jiahuangxianjunzuo (JHXJZ). Moreover, the effects of JHXJZ on ergosterol content, membrane permeability, cell structure and seven key genes involved in the ergosterol biosynthetic pathway were investigated. JHXJZ had a strong anti-fungal activity against L. theobromae in vitro, with an EC50 of 3.54 ± 0.55 µg/mL, and its curative efficacies on detached tea leaves reached 41.78% at 100 µg/mL, respectively. JHXJZ up-regulated 899 genes (P < 0.05) and down-regulated 1,185 genes (P < 0.05) in L. theobromae. These genes were found to be associated with carbohydrate metabolic processes, which are closely related to steroid biosynthesis in the KEGG pathways. Because JHXJZ regulates the key genes of sterol biosynthesis, it decreased the ergosterol content, increased cell-membrane permeability, changed the cellular structure, the enhanced roughness of surface of the hyphae, and resulted in degradation of the hyphal nuclei and necrosis of the hyphal cytoplasm.