BACKGROUNDContinuous use of synthetic bactericides and fungicides is causing pathogens to develop resistance, resulting in increased use of pesticides and affecting food security. The green pesticides derived from natural products could reduce or avoid ‘pesticide hazards’ caused by synthetic pesticides as a result of their unique mechanism of action. Therefore, it is of great significance to create green pesticides with novel structures.RESULTSHerein, 30 novel myricetin derivatives containing piperidine and amide fragments were designed and synthesized using active group splicing. Among them, compound Z30 had excellent inhibitory effect against Xanthomonas oryzae pv. Oryzae (Xoo) with the half effective concentration (EC50) of 2.7 μg mL−1. Compound Z26 not only exhibited better antibacterial activity against Xaxonopodis pv. Citri (Xac) with EC50 of 3.9 μg mL−1, but also displayed higher antifungal activity against Rhizoctonia solani (Rs) with EC50 of 8.3 μg mL−1. In vivo experiments proved that Z30 against bacterial blight of rice and Z26 against rice blast exhibits significant protective and curative effect. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed that Z26 and Z30 could change the integrity of cell wall and membrane of pathogen Xoo, Xac and Rs, resulting in cytoplasmic leakage and eventually death. Enzymatic assay, molecular docking and molecular dynamics simulations (MDs) indicated that Z26 could be used as a potential succinate dehydrogenase inhibitor (SDHI).CONCLUSIONZ26 and Z30 significantly reduced the pathogenicity of the pathogens, which provided a new idea and direction for the development of green pesticides. © 2023 Society of Chemical Industry.