In an attempt to search for natural renewable product-based antifungal agents, eighteen 1,3,4-thiadiazole-urea compounds containing gem-dimethylcyclopropane ring structure were designed and synthesized. The antifungal activity of the target compounds against six plant pathogens was preliminarily evaluated at the concentration of 50 mg/L. As a result, the inhibitory rates of (+)-cis-1-(4-bromophenyl)-3-(5-((2,2-dimethyl-3-propylcyclopropyl)methyl)-1,3,4-thiadiazol-2-yl) urea (7i) against Colletotrichum orbicular, Bipolaris maydis and Alternaria solani were 91.2%, 85.0% and 60.1%, respectively, which was better than that of the positive control chlorothalonil. Furthermore, a reasonable and effective 3D-quantitative structure-activity relationship (3D-QSAR) model (r 2 =0.990, q 2 =0.517) was established by the comparative molecular field analysis method (CoMFA). The binding mode between the target compounds and succinate dehydrogenase (SDH) was investigated by molecular docking, and the cation-π interaction between the key residue Arg and the benzene ring was quantitatively analyzed. The gem-dimethylcyclopropane and thiadiazole-urea-benzene moieties of the target compounds probably made major contributions to the antifungal activity by frontier molecular orbital calculation.