Global warming and extremely high temperatures affect insect survival and distribution. In this study, we characterized the gene expression profiles of red (PAR) and green (PAG) morphs of the pea aphid (Acyrthosiphon pisum) at three high temperatures (30 °C, 36 °C, and 38 °C) and three treatment durations (6 h, 12 h, and 24 h) by high-throughput sequencing. Both PARs and PAGs increased the number of significantly differentially expressed genes as temperature and treatment duration increased, particularly for genes associated with stress resistance, lipid metabolism, cuticular protein expression, and the initiation of various regulatory mechanisms. However, the response mechanisms and their intensities varied between the morphs. More cuticular protein genes were down-regulated in PAGs, while more stress resistance genes up-regulated in PARs. JAK-STAT, MAPK, Estrogen, Insulin signaling, and Longevity-regulating pathways were enriched in PARs, whereas AMPK, Insulin signaling, and Circadian rhythm pathways were enriched in PAGs. These results suggested that PARs possesses greater adaptability than PAGs under extreme high temperatures. The different temperature adaptability between morphs may represent an ecological strategy developed by A. pisum to adapt to global warming. This research enhances our understanding of the mechanisms underlying insect survival in high-temperatures environments and provides guidance for the development of control strategies.