The jumbo flying squid, Dosidicus gigas, is an economically important squid species with a short life cycle. It is widely distributed in the Eastern Pacific Ocean and is exploited by international fishing vessels, such as those from Peru, Chile, and China. The inter-annual catch of D. gigas fluctuated significantly from year to year and was closely related to environmental changes and climate variability. Previous studies have found that fluctuations in the catch of this squid are associated with local environmental conditions such as sea surface temperature, current, and food density. However, this species exhibits vertical migration, and changes in the water temperature at different depths tend to have a significant impact on their resource abundance and habitat distribution. Therefore, to evaluate the impact of vertical water temperature on the habitat changes of D. gigas in the Southeast Pacific Ocean off Peru, a habitat suitability index model (HSI) was established. This model utilized the fisheries data of D. gigas in the spring and summer seasons off Peru from 2006 to 2015 (September to February of the next year), combined with the vertical water temperature data at depths of 0 m, 50 m, 100 m, and 150 m, to analyze the spatial and temporal distribution of the fishery and habitat of D. gigas off Peru. Fisheries data were obtained from the National Distant-Water Fisheries Data Center of China. By calculating the percentage of HSI in suitable habitats and validating the model with data from 2014-2015, the habitat model based on the vertical water temperature factor and the arithmetic mean method could better simulate HSI values. The results of the spatial correlation analysis showed that the water temperature at each water layer off Peru was negatively correlated with habitat suitability. Changes in catch per unit effort and suitable habitat area for D. gigas were relatively minor, with no significant inter-annual or inter-monthly differences, and a significant positive correlation was observed between them. However, significant inter-annual and inter-monthly changes were observed in the gravity center of the fishing effort and habitat of D. gigas, which showed a similar tendency to move in a southeastern direction. Moreover, a significant reduction was observed in the area of suitable habitats in spring compared to summer. The monthly and inter-annual changes in the longitudinal and latitudinal gravity centers of the fishing grounds of D. gigas were consistent with the spatial distribution of the habitat. A significant positive correlation was observed between these two variables. This study demonstrated a close correlation between the abundance of D. gigas and the extent of suitable habitat. Significant inter-annual and inter-monthly variations in the suitable habitat of D. gigas were identified, serving as a crucial factor in the spatial and temporal distribution variations of D. gigas off Peru. This finding suggests that vertical water temperature should be considered when evaluating the habitat changes of D. gigas in the Southeast Pacific Ocean off Peru.