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Background: Plant diseases caused by plant pathogens are important constraints to agricultural production throughout the world and at least 10% of global food production is lost to plant diseases. In order to discover new fungicides and control the plant diseases, a series of novel 1,2,4- triazole thioether derivatives carrying a pyrimidine moiety were designed and synthesized. Methods: Thirteen novel 1,2,4-triazole thioether derivatives carrying a pyrimidine moiety were designed by splicing the active substructure and synthesized under microwave irradiation condition. Their structures were characterized by 1H-NMR, 13C-NMR, ESI-MS and elemental analysis, and their antifungal activities were evaluated using the mycelium growth rate test. Results: These compounds were screened for antifungal activity against Colletotrichum orbiculare, Botrytis cinerea and Rhizoctonia solani at 50 μg/mL. Some compounds showed moderate to good antifungal activities. Especially the inhibition rate of compound 7c against C. orbiculare and R. solani were 80% and 76% respectively. Conclusion: A practical synthetic route to 1,2,4-triazole thioether derivatives by using the microwave- assisted method is presented. This study suggests that the 1,2,4-triazole thioether derivatives exhibited moderate to good inhibition activity against C. orbiculare and R. solani at 50 μg/mL, and could be further developed as potential fungicides.