As a powerful sanitizer, chlorine dioxide (ClO₂) has mainly focused on control of bacteria, but little is known about its antifungal effects, especially on postharvest fungi found in vegetable and fruit. This study investigated the effect of ClO₂ on Botrytis cinerea growth in vitro and on its disease severity in green pepper and winter jujube. Result showed that ClO₂ fumigation reduced disease development of grey mold caused by B. cinerea on green pepper and winter jujube, and the efficiency was positively correlated with ClO₂ concentrations. ClO₂treatment directly inhibited mycelial growth, spore germination and germ tube elongation of B. cinerea. To further survey the mechanisms by which ClO₂ treatment inhibited hypha growth of B. cinerea, we observed the mycelial morphology and the integrity of the plasma membrane; the results showed that ClO₂ treatment resulting in B. cinerea mycelial morphology was strongly affected, and leading to the loss of plasma membrane integrity, causing the cellular leakage. These data showed that ClO₂ was effective for controlling grey mold caused by B. cinerea on green pepper and winter jujube, and the antifungal activity of ClO₂ could be attributed to the disruption of cell membrane of the fungal pathogen.