24 chalcone derivatives containing 1,3,4-thiadiazole were synthesized. The results of bioactivity tests indicated that some of the target compounds exhibited superior antifungal activities in vitro. Notably, the EC50 value of D4 was 14.4 µg/mL against Phomopsis sp, which was significantly better than that of azoxystrobin (32.2 µg/mL) and fluopyram (54.2 µg/mL). The in vivo protective activity of D4 against Phomopsis sp on kiwifruit (71.2%) was significantly superior to azoxystrobin (62.8%) at 200 µg/mL. The in vivo protective activities of D4 were 74.4 and 57.6% against Rhizoctonia solani on rice leaf sheaths and rice leaves, respectively, which were slightly better than those of azoxystrobin (72.1 and 49.2%) at 200 µg/mL. Scanning electron microscopy (SEM) results showed that the mycelial surface collapsed, contracted and grew abnormally after D4 treatment. Finally, the results were further verified by in vivo antifungal assay, fluorescence microscopy (FM) observation, determination of relative conductivity, membrane lipid peroxidation degree assay, and determination of cytoplasmic content leakage. Molecular docking results suggested that D4 could be a potential SDHI.