Exploring the synchronization of species habitat changes within an area is beneficial to the effective utilization and management of multiple associated species resources. In this study, we used fisheries and environmental (including sea surface height anomaly (SSHA), sea surface salinity (SSS), and 400 m water layer temperature (Temp_ 400 m) data on Dosidicus gigas in the autumns of 2011–2016, and fisheries and environmental (including sea surface temperature (SST), mixed layer depth (MLD), and 400 m water layer temperature (Temp_ 400 m) data on Trachurus murphyi in the autumns of 2013–2016 to construct habitat models with different weights. The optimal habitat models were selected and validated by data from 2017. Based on the highest performing model, the habitat suitability indices of Trachurus murphyi and Dosidicus gigas were predicted from 1950 to 2017, with differences in habitat changes between the species further examined under different ENSO events. The results showed that the optimal model of Trachurus murphyi and Dosidicus gigas could accurately predict their potential distribution. During the El Ni?o years, the sea surface temperature was higher, the sea surface height decreased from northeast to southwest, the mixed layer depth was shallow, and the sea surface salinity concentration in the north of Chile were higher than those in the South; the species distribution results showed that suitable habitats for Trachurus murphyi significantly increased and the gravity center of the optimal HSI moved westward, while suitable habitats for Dosidicus gigas decreased and the gravity center of the optimal HSI moved southeast. During the La Ni?a years, sea surface temperature was lower, the sea surface height increased from northeast to southwest, the mixing layer depth was increased, and the sea surface salinity was similar to that during El Ni?o years, though the difference was not significant; under tHSI climate conditions, suitable habitats for Dosidicus gigas increased significantly in a latitudinal direction and the gravity center of HSI moved northeastward, while the suitable habitats for Trachurus murphyi decreased significantly in a southwesterly direction and the optimal HSI weight was heavy, indicating a core habitat shifts to the southeast. Our findings suggest that variations in the suitable habitats of Trachurus murphyi and Dosidicus gigas under different ENSO events may be related to current distributions in the Southeast Pacific Ocean and prey biomass prey.