The jumbo flying squid Dosidicus gigas is an environmentally sensitive cephalopod. The habitat variation of D. gigas is greatly affected by multi-scale climate variability. In this study, we constructed a habitat suitability index (HSI) model based on two critical environmental variables (sea surface temperature (SST) and sea surface height (SSHA) from 1950 to 2015), and analyzed seasonal habitat distribution for D. gigas off Peru under different climate conditions. The results suggested that habitat suitability during the cold Pacific Decadal Oscillation (PDO) was higher than that during the warm PDO. Compared with the cold PDO, suitable D. gigas habitat during the warm PDO shifted southeastward. The spatial distribution of suitable habitat was consistent with the overlapping areas of both the suitable SST and SSHA ranges, indicating that the two critical environmental variables were significantly related to the spatial distribution of suitable habitats. Moreover, the HSI anomalies on the D. gigas fishing ground were significantly negatively correlated with the PDO index. The habitat suitability on the D. gigas fishing ground in spring was higher than that in winter, and the spatial distribution of suitable habitat in winter was further Southeast than that in spring. The longitudinal and latitudinal distribution of suitable SST and the most suitable SST on the fishing ground of D. gigas showed significant variability between June and November. The distribution of the most suitable SST in spring (September to November) shifted northwestward; however, the distribution of the most suitable SST in winter (June to August) shifted southeastward. The difference in seasonal habitat distribution for D. gigas under different climate conditions may be owing to the monthly difference in distribution of the most suitable SST. Our findings indicated that there were significant differences in the habitat suitability on D. gigas fishing grounds under different PDO periods, and the difference in seasonal distribution could be explained by monthly differences in environmental variables.