Temperature is a major environmental factor that affects fruit storage, but the underlying molecular mechanism is poorly understood. Here, the differences in transcriptome, ethylene production, pulp softening of postharvest peach fruits were compared between common and high temperature storage conditions. High temperature storage resulted in a lower level of ethylene production and a slower fruit softening due to the decreased expression levels of ethylene biosynthetic genes and softening related enzymes. The MEKK1-MKK2-MPK4/6 genes had high expression levels in response to high temperature condition. The decreased expression of pectinesterase, polygalacturonase, pectate lyase, pectin methylesterase and the increased expression of expansin were observed in high temperature treatment. A series of genes related to membrane stability also showed lower transcription levels, such as peroxidase, lipoxygenase 3 and superoxide dismutase 1/2. These genes were co-expressed with different auxin response factors, ethylene response factors and they composed function modules collectively correlated to physiological changes. Finally, we proposed a model of the molecular response mechanism of peach fruit at high temperature which helps to develop new approaches for maintaining fruit quality during storage.