A series of pyrimidine-containing 4H-chromen-4-one derivatives were designed and synthesized by combining bioactive substructures. All compounds were characterized using 1 H NMR, 13 C NMR, 19 F NMR and HRMS. Preliminary biological activity results showed that most of title compounds displayed signi cant inhibitory activity against Xanthomonas axonopodis pv. Citri (Xac), Xanthomonas oryzae pv. oryzae (Xoo) and Ralstonia solanacearum (Rs). In particular, compound 4c demonstrated a good inhibitory effect against Xac and Xoo, with half-maximal effective concentration(EC 50 ) values of 15.5 and 14.9 μg/mL respectively, and that of compound 4h showed the best antibacterial activity against Rs with an EC 50 value of 14.7 μg/mL, These results were better than both bismerthiazol (BT, 51.7, 70.1 and 52.7 μg/mL, respectively) and thiodiazole copper (TC, 77.9, 95.8 and 72.1 μg/mL respectively). In vivo antibacterial activity results indicated that compound 4c displayed better curative(42.4%) and protective (49.2%) activities for reducing rice bacterial leaf blight than both BT (35.2, 39.1%) and TC (30.8, 27.3%). The mechanism of compound 4c against Xoo was analysed through scanning electron microscopy (SEM). Results showed that the compound destroied the bacterial cell membrane structure. These results indicated that pyrimidine-containing 4H-chromen-4-one derivatives are valuable in the research of new agrochemicals.