The jumbo flying squid Dosidicus gigas, which is widely distributed in the eastern Pacific Ocean, has been regarded as an important fishing target for Chinese distant-water fisheries. Previous studies have linked the fluctuations in squid catch to varying local environmental conditions and climate shifts, such as sea surface temperature, chlorophyll-a, and El Niño-Southern Oscillation. As a short-lived cephalopod, D. gigas is sensitive to environmental changes caused by climatic events, leading to changes in both the spatial and temporal distribution of its habitats. The Pacific Decadal Oscillation (PDO) is a strong indicator reflecting climate and environmental changes occurring across interdecadal time scales within the Pacific region. Though the oscillation between the warm and cold phases of the PDO can affect the marine ecosystem and fishery industry in the Pacific Ocean, limited research has been conducted on its effect on short-lived cephalopod species, particularly D. gigas. In addition, D. gigas has a diurnal vertical migration pattern, which is influenced by water temperature. Studies have demonstrated that employing a habitat model that incorporates vertical water temperature factors leads to improved simulation and prediction of the distribution of D. gigas habitats. In this study, we aimed to analyze the long-term changes in the vertical water temperature and suitable habitat of D. gigas in different PDO periods. We calculated the suitability index (SI) of vertical water temperature and the habitat suitability index (HSI) of D. gigas from 1950 to 2015 off Peru using four key water temperature factors at 0, 50, 100, and 150 m. The water temperatures at all four depths in the Peruvian waters were significantly higher during the warm phase of the PDO than those during the cold PDO phase. The HSI observed on the fishing ground displayed a significant negative correlation with the PDO index. In the cold phase of the PDO, the vertical water temperature off Peru experienced cooling, leading to higher quality habitat for D. gigas. This shift caused the favorable water temperature range to move northwestward, inducing an increase in the habitat suitability. The suitable habitat expanded and shifted northwestward. However, during the warm phase of PDO, vertical water temperatures increased, which was unfavorable to the growth of D. gigas. Moreover, the suitable water temperatures range decreased, resulting in lower HSI and a southeastward shift of suitable habitat. In addition, there were significant seasonal variations in the suitable habitat of D. gigas. In contrast to spring, HSI exhibited higher levels during summer, which coincided with expansion of suitable habitat towards northeast. Our findings suggested that spatio-temporal distribution of D. gigas habitat is closely related to the changes in seawater temperature at different water layers driven by the PDO phase shift. Moreover, there are clear seasonal variations in the distribution of this habitat.