Latent infection was analyzed when harpin at 50 mg/L was sprayed on muskmelon 4 times at four different stages: florescence, young fruit, fruit enlarging, and netting periods. Results showed that the latent infection was significantly lower in sprayed muskmelons than in the control fruit. Meanwhile, the activities of peroxidase, phenylalanine ammonia-lyase, β-1,3-glucanase, and chitinase increased significantly in the fruit treated with harpin. It also resulted in an increase of contents of total phenolic compounds, flavanoids, and lignin. In addition, the treatment of harpin increased the activity of superoxide dismutase, enhanced the content of hydrogen peroxide, and reduced catalase activity. Furthermore, harpin treatments contributed to the reinforcement of cell walls of pericarp in fruit, the reduction of postharvest decay, and the improvement of postharvest qualities. These results suggested that harpin effectively participated in inducing resistance and could be a new strategy for preventing latent infection in muskmelon.