In order to explore novel antibacterial agents, a series of newly designed and synthesized 1,3,4-oxadiazole derivatives (series X) and 1,2,4-triazole derivatives (series M) incorporating disulfide bond were subjected to antibacterial activities evaluation. Interestingly, both series X and series M showed good antibacterial activity against Xanthomonas oryzae pv. Oryzae (Xoo). Among them, 3-(5-(isobutyldisulfaneyl)-4H-1,2,4-triazol-3-yl)-1H-indole (M1) exhibited potent antibacterial activity against Xoo, with EC50 value of (1.51 +/- 0.24) mu g/mL, surpassing those of thiodiazole copper [(87.97 +/- 4.79) mu g/mL] and bismerthiazol [(66.88 +/- 4.06) mu g/mL]. In rice plants, compound M1 exhibited superior antibacterial activity to the bismerthiazol. The curative and protective effects of compound M1 on rice were 42.37% and 38.64%, respectively, surpassing the curative and protective effects of bismerthiazol (37.49% and 36.55%). Furthermore, through relevant studies on the mechanism of compound M1, it was demonstrated that compound M1 inhibits the formation of biofilms in Xoo, elevates the level of reactive oxygen species in the bacteria, and induces morphological changes. Proteomic analysis revealed that compound M1 down-regulated the adenosine triphosphate-binding cassette (ABC) transporters, which impacts adenosine triphosphate (ATP) decomposition and phosphorus transport in rice bacterial blight. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) demonstrated that compound M1 was experimentally antibacterial by down-regulating related genes in the phosphate special transport (pst) system of the ABC transporters.