The effect of chitosan treatment alone or in combination with methyl jasmonate (MeJA) against Alternaria alternata in vitro and in vivo, and defense related enzyme activities were investigated. 100–500 μl/l MeJA significantly inhibited mycelial growth of A. alternata. The inhibitory activity of MeJA on mycelial growth, spore production, spore germination and germ tube length of A. alternata in vitro could be enhanced by 0.1% chitosan. The combination of 0.1% chitosan and 500 μl/l methyl jasmonate was more effective to reduce the disease incidence and lesion diameter of postharvest decay of cherry tomato than the application of MeJA or chitosan alone. The combined treatments resulted in higher activities of PPO (polyphenol oxidase), POD (peroxidase) and PAL (phenylalanine ammonialyase) than the control. This work indicated that the combination of chitosan and methyl jasmonate is a promising method to control postharvest decays of fruit and vegetables.