Neon flying squid (Ommastrephes bartramii) is a large pelagic squid internationally harvested in the North Pacific. Here, we examined its potential habitat in the central North Pacific using an ensemble modelling approach. Initially, ten statistical models were constructed by combining the squid fishing points, selected vertical layers of the sea temperature and salinity, sea surface height (SSH), and SSH gradient from the multi-variate ocean variational estimation system for the western North Pacific from June to July 1999–2011. The variable selection analyses have captured the importance of vertical temperature and salinity layers at the upper 300 and 440 m, respectively, coinciding with the reported vertical ranges of diel migration for the squid's primary prey species in the North Pacific. The evaluation of the habitat predictions using the independent sets of the presence data from 2012 to 2014 showed significant variability in the predictive accuracy, which is likely reflective of the interannual differences in environmental conditions across the validation periods. Our findings from ensemble habitat model approach using three-dimensional oceanographic data were able to characterize the near- and subsurface habitats of the neon flying squid. Moreover, our results underpinned the possible link between interannual environmental variability and spatio-temporal patterns of potential squid habitats. As such, these further suggest that an ensemble model approach could present a promising tool for operational fishery application and squid resource management.