The antifungal activity of nonanal against Botrytis cinerea, one of the most important postharvest diseases of tomato gray mold, was tested by in vitro and in vivo experiments. Results of in vivo tests demonstrated that wax + nonanal treatment significantly decreased the incidence of gray mold during the entire storage period. After 8 d of storage, the disease incidences in Wax + nonanal (1×, 4× or 10× MFC)-treated fruits were 46.7%, 56.7%, 73.3%, respectively, in contrast to 100% of the control fruits. Loss of membrane integrity was examined and quantified under 10×MFC nonanal condition by the method of propidium iodide fluorescent staining. Wax + nonanal (10×MFC) treatment remarkably increased antioxidant enzyme activities, such as catalase (CAT), superoxidase dismutase (SOD), peroxidase (POD) and phenylalanine ammonia lyase (PAL). Meanwhile, this treatment (10×MFC) evidently exhibited a delayed decline in antioxidant enzyme activities. Furthermore, nonanal treatment retained the fruit quality of tomatoes because it reduced the coloration index and weight loss and retained fruit firmness. No significant differences were found between the pH, Firmness and total soluble solid (TSS) content for all treatment under the same storage time. Our results suggest that nonanal can be considered as a good alternative to conventional fungicides in controlling the decay of tomato fruits.