The Sardinops melanostictus and the Scomber japonicus are important economic species in the northwestn Pacific Ocean, and exploring the correlation between their habitat changes is conducive to the rational development and management of fishery resources. This study utilizes fishery data of Sardinops melanostictus and Scomber japonicus in the northwestern Pacific Ocean from June to November between 2017 and 2021. By incorporating three key environmental variables, namely sea surface temperature, sea surface height, and chlorophyll a mass concentration, habitat models with different weights are constructed. The models are then validated using fishery data from 2021. The optimal models are selected to predict the most suitable habitat distribution of Sardinops melanostictus and Scomber japonicus under different El Niño-Southern Oscillation (ENSO) events. The study analyzes the differences and synchronicity in the spatial and temporal distribution of the most suitable habitat between the two species under different ENSO events. The results indicate that the suitable habitat area of Sardinops melanostictus (above 15%) was higher than that of Scomber japonicus (less than 6%) under different ENSO events; however, the growth rate of the most suitable habitat area for Sardinops melanostictus under La Niña events is higher than that of El Niño events. The former has a growth rate of 0.197 and the latter has a growth rate of 0.123, on the contrary, the growth rate of Scomber japonicus under the La Niña event is lower than that of El Niño event, the former has a growth rate of 1.114 and the latter has a growth rate of 2.082; additionally, when the distribution locations of Sardinops melanostictus and Scomber japonicus are close to each other, it promotes favorable conditions for their habitats. On the other hand, when the distribution locations are far apart, it somewhat inhibits the increase in the suitable habitat area for Scomber japonicus. The co-variation of suitable habitat areas for Sardinops melanostictus and Scomber japonicus under different ENSO events may be related to their interspecies relationship (competition/predation-prey) and the distribution of ocean currents in the northwestern Pacific Ocean.