Hongmeiren citrus, an economically important fruit, currently lacks targeted measures to control postharvest decay. While durian shells are rich in diverse antimicrobial compounds, their antifungal potential remains underexplored. In this study, Fusarium oxysporum was identified as a dominant pathogen causing rot in Hongmeiren citrus. We then evaluated the antifungal efficacy of durian shell water extract (DSWE) against F. oxysporum in vitro and further elucidated the underlying inhibitory mechanism through molecular docking analysis. Our results demonstrated that treatment with 4 mg/mL DSWE significantly reduced mycelial growth diameter by 77.2 % and completely suppressed sporulation by the 6th day post-inoculation, compared to the control (CK). Propidium iodide (PI) staining and scanning electron microscopy (SEM) revealed severe membrane damage and hyphal collapse in F. oxysporum treated with 4 mg/mL DSWE. Molecular docking predicted that three bioactive compounds in DSWE (fraxetin, taxifolin, and muscone) could bind to key proteins involved in the cell wall and membrane biosynthesis of F. oxysporum. Experimental validation confirmed that fraxetin, taxifolin, and muscone reduced the colony diameter of F. oxysporum by 62.8 %, 53.2 %, and 21.1 %, respectively, while inducing significant membrane injury. Notably, fraxetin and taxifolin exhibited superior antifungal activity compared to muscone. This study elucidates the mechanism by which DSWE inhibits F. oxysporum and highlights its potential as an eco-friendly strategy for controlling postharvest pathogens in citrus.