Harpin protein enhances plant disease resistance by activating PAMP-induced immunity. In this study, applications of harpin enhanced the efficiency of photosystem II, resulting in an increase in the fresh weights of Phalaenopsis orchids. A transcriptomic study of these harpin-treated Phalaenopsis orchids revealed that the application of harpin activated the expression of genes involved in nitric oxide (NO) generation, secondary metabolite production and plant responses, including responses to biotic, light stress, senescence, and hypoxia stimuli. Moreover, exposure to harpin induced the expression of a nitrate transporter and different members of the jasmonic acid resistance family. A proteomic study indicated that harpin applications increased protein accumulation in Phalaenopsis leaf tissues, including the accumulations of Cu/Zn superoxide dismutase (CSD2), pathogenesis-related protein 2, plasma membrane H+-ATPase, and protochlorophyllide oxidoreductase. In summary, this study demonstrates the effects of harpin on defense activation and growth promotion in Phalaenopsis orchids at both the physiological and molecular levels. Moreover, our study demonstrates that harpin modulates plant gene expression, most likely through its effects on reactive oxygen species (ROS), NO, and jasmonic acid signaling pathways.