AbstractBACKGROUNDPydiflumetofen, as a new succinate dehydrogenase inhibitor (SDHI) chiral fungicide, has been used in crop production because of its broad‐spectrum and high‐efficiency antifungal activity. However, little is known about pydiflumetofen at the chiral level. The stereoselective bioactivity and degradation of pydiflumetofen enantiomers were therefore investigated.RESULTSPydiflumetofen presented effective bioactivity against the eight tested phytopathogens, and its enantiomers showed significant differences in activity. The bioactivity of R‐pydiflumetofen was 9.0–958.8 times higher than that of the S enantiomer. Treatment with R‐pydiflumetofen increased the cell membrane permeability of Sclerotinia sclerotiorum and decreased exopolysaccharide and oxalic acid production more than treatment with S‐pydiflumetofen. Furthermore, R‐pydflumetofen exhibited better inhibitory activity against the succinate dehydrogenase enzyme of S. sclerotiorum than S‐pydiflumetofen by 584‐fold. According to homology modeling and molecular docking studies, the binding affinities of the R and S enantiomers were −7.0 and −5.3 kcal mol−1, respectively. Additionally, the degradation half‐lives of S‐ and R‐pydiflumetofen in three vegetables (cucumber, eggplant, and cowpea) under field conditions were 2.56–3.12 days and 2.48–2.76 days, respectively, which reveals that R‐pydiflumetofen degrades faster than S‐pydiflumetofen.CONCLUSIONBased on the results obtained, R‐pydiflumetofen not only exhibited a higher bactericidal activity, but also posed fewer residual risks in the environment. The mechanism of the stereoselective bioactivity was correlated with the stereoselective inhibition activity of the target enzyme and affected the cell membrane permeability and the production of exopolysaccharide and oxalic acid. This research could provide a foundation for the systematic evaluation of pydiflumetofen from an enantiomeric view. © 2021 Society of Chemical Industry.