Botrytis cinerea is one of the most devastating pathogen responsible for postharvest decay of fresh fruits and vegetables. However, traditional fungicide application is inclined to develop resistance strains, complicating the control of gray mold. Hence, there is an urgent need for exploiting new antifungal active substances and enhancing their antifungal activity in an environmentally friendly manner. In this study, tropolone was demonstrated efficacy in inhibiting B. cinerea mycelial growth at relatively low (40 mg L⁻¹) tropolone concentrations and spore germination at even lower (10 mg L⁻¹) tropolone concentrations. The antifungal mechanisms were linked to the disruption of spore germination-related gene expression rather than directly killing B. cinerea through cell membrane disruption. The inhibition of spore germination hindered the penetration of B. cinerea into host cells, thereby reducing disease severity in harvested apples and strawberries. To increase the protective effect of tropolone, we prepared small-sized maize starch nanoparticles loaded with tropolone and confirmed an enhanced antifungal effect. This study provides a theoretical foundation for the application of small-sized maize starch nanoparticles to increase antifungal effect and reduce fungicide application in postharvest disease control.