Jiash melon and 86-1 melon were used as experiment material in this paper. After inoculated with Alternaria alternata by injury, the differences between the two were compared in terms of lesion diameter, pathogen-induced plant protein and protective enzyme activity. The results showed that the lesions of Jiashi melon were less than 86-1, and the diameter of the pericarp was smaller than the sarcocarp. After inoculated with Alternaria alternata, pathogen-induced plant protein and protective enzyme activity of two melons were increased during whole storage period. It played an important role in resisting the infection of Alternaria alternata, especially in the middle and late stages of infection. The activity of inoculated pericarp and sarcocarp in Jiashi melon was higher than 86-1 melon.