Neopeltolide, a natural product isolated from deep-water sponge specimen of the family neopeltidae, has been proven to be a novel inhibitor of cytochrome bc. In this study, a series of neopeltolide derivatives was designed by replacing the 14-membered macrolactone with indole ring and confirmed by H NMR, C NMR, and HRMS. Based on the binding mode of 12h with bc complex, the IC values of compounds 16a-f (ranging from 0.70 to 1.46 μM) were improved significantly than the ester derivatives 12a-u by replacing the ester with amide linker. Subsequently, the molecular docking results indicated that compound 16e could form a π-π interaction with Phe274 and two H-bonds with Glu271 and His161 and the latter H-bond was found to account for its high activity. The present work accelerates the discovery of novel bc complex inhibitors to deal with the resistance that the existing bc complex inhibitors are facing and provides a valuable idea for the design of new fungicides.