In this study, 12 pairs of tautomeric flavonol derivatives containing quinoxaline were synthesized. The results of antifungal activity showed that in the enol−keto tautomerism, the target compounds containing keto (Y B series) had better inhibitory activity against Sclerotinia sclerotiorum (S.s.) than compounds containing enol (Y A series). Y B9 showed the strongest antifungal activity against S.s., and the median effective concentration (EC 50 ) value was 1.0 μg/mL, which was better than azoxystrobin (Az, 35.3 μg/mL). In vivo fungal inhibition experiments showed that the protective activity of Y B9 against rape leaves was 83.4% at 200 μg/mL, which was superior to that of Az (70.2%). The activity of succinate dehydrogenase and molecular docking results showed that Y B9 had a stronger antifungal effect than Y A9 . The results of oxalic acid content determination showed that Y B9 could reduce the pathogenic ability of S.s. Then, the inhibitory effect of Y B9 against S.s. was further verified by scanning electron microscopy, fluorescence microscopy, cell membrane permeability, cell content leakage, and malondialdehyde content.