Understanding the stereoselective bioactivity of chiral pesticides is crucial for accurately evaluating their effectiveness and optimizing their use. Isopyrazam, a widely used chiral SDHI fungicide, has been studied for its antifungal activity only at the racemic level. Therefore, to clarify the highly bioactive isomers, the stereoselective bioactivity of isopyrazam isomers against four typical phytopathogens was studied for the first time. The bioactivity ranking of the isomers was trans-1S,4R,9R-(+)-isopyrazam > cis-1R,4S,9R-(+)-isopyrazam > trans-1R,4S,9S-(-)-isopyrazam > cis-1S,4R,9S-(-)-isopyrazam. SDH activity was assessed by molecular docking simulation and actual detection to confirm the reasons for stereoselective bioactivity. The results suggest that the stereoselective bioactivity of isopyrazam is largely dependent on the differential binding ability of each isomer to the SDH ubiquitin-binding site, located within a cavity formed by the iron-sulfur subunit, the cytochrome b560 subunit, and the cytochrome b small subunit. Moreover, to reveal the molecular mechanism of isopyrazam stereoselectively affecting mycelial growth, the contents of succinic acid, fumaric acid, and ATP were measured. Furthermore, by measuring exospore polysaccharides and oxalic acid content, it was determined that 1S,4R,9R-(+)- and 1R,4S,9R-(+)-isopyrazam more strongly inhibited the ability of Sclerotinia sclerotiorum to infect plants. The findings provided essential data for the development of high-efficiency isopyrazam fungicides and offered a methodological reference for analyzing the enantioselective activity mechanism of SDHI fungicides.