BACKGROUNDSclerotinia stem rot caused by Sclerotinia sclerotiorum seriously endangers oilseed rape production worldwide, and the occurrence of fungicide‐resistant mutants of S. sclerotiorum leads to control decline. Thus, it is critical to explore new green substitutes with different action mechanisms and high antifungal activity. Herein, the activity and the action mechanism of natamycin against S. sclerotiorum were evaluated.RESULTSNatamycin showed potent inhibition on the mycelial growth of S. sclerotiorum, and half‐maximal effective concentration (EC50) values against 103 S. sclerotiorum strains ranged from 0.53 to 4.04 μg/mL (mean 1.44 μg/mL). Natamycin also exhibited high efficacy against both carbendazim‐ and dimethachlone‐resistant strains of S. sclerotiorum on detached oilseed rape leaves. No cross‐resistance was detected between natamycin and carbendazim. Natamycin markedly disrupted hyphal form, sclerotia formation, integrity of the cell membrane, and reduced the content of oxalic acid and ergosterol, whereas it increased the reactive oxygen species (ROS) and malondialdehyde content. Interestingly, exogenous addition of ergosterol could reduce the inhibition of natamycin against S. sclerotiorum. Importantly, natamycin significantly inhibited expression of the Cyp51 gene, which is contrary to results for the triazole fungicide flusilazole, indicating a different action mechanism from triazole fungicides.CONCLUSIONNatamycin is a promising effective candidate for the resistance management of S. sclerotiorum. © 2023 Society of Chemical Industry.