Succinate dehydrogenase (SDH) is an important target enzyme for designing agricultural chemical fungicides. In order to explore novel natural product‐based antifungal agents, twenty‐one unreported anisaldehyde‐derived amide‐thiourea compounds were designed and synthesized using the principle of active splicing, and structurally confirmed by 1H‐NMR, 13C‐NMR, ESI‐MS, FT‐IR, and element analysis. In vitro antifungal activity of the target compounds was evaluated by the agar dilution method. The results showed that some target compounds exhibited better or comparable antifungal activity than that of the commercial fungicide chlorothalonil, in which compounds 5c, 5o, and 5r displayed excellent antifungal activity of 92.6 %, 92.6 % and 99.1 % against P. piricola, respectively, better than that of the positive control. In addition, 3D‐QSAR analysis was carried out by the CoMFA method to reveal the relationship between the structures of the target compounds and their inhibitory activities. The simulative binding mode of the target compounds and SDH was also studied by molecular docking.