Powdery mildew is a major fungal disease affecting melon production, and analyzing the molecular regulatory mechanism of resistance in melon is a prerequisite for melon molecular breeding of powdery mildew resistance. In this study, a resistant melon material was selected for inoculation and sterile water control treatments, and four time points, 0 h, 24 h, 48 h and 72 h after treatment, were selected for transcriptome sequencing analysis. The content of disease resistance related hormones was also determined and WGCNA analysis was performed. The results showed that allantoin and jasmonic acid were related to the regulation of powdery mildew resistance in melon, and key genes responding to the disease resistance response were found. In this study, we found that powdery mildew infested melon leaves induced a rise in the content of allantoin, which in turn induced a rise in the content of jasmonic acid and induced the accumulation of reactive oxygen species and thus resistance through the signaling of Ca2+ and WRKY transcription factors. This study initially explored the molecular regulatory mechanism of powdery mildew resistance in melon and provided a theoretical basis for molecular breeding of powdery mildew resistance in melon.