The neon flying squid Ommastrephes bartramii from is a migratory ommastrephidae squid species with ecological importance and economic values. At present, O. bartramii is mainly targeted by the squid-jigging fishing vessels from Japan, ROK and China and so on. O. bartramii has only 1-year life span, therefore, its habitat suitability is largely affected by climate variability and environmental conditions. In this study, an integrated habitat suitability index (HSI) model was developed based on the fishing effort and the arithmetic mean method by using the fisheries data from September to November during 2006-2015 obtained from the data centers of Chinese squid-jigging fishery combined with two key environmental variables including sea surface temperature (SST) and photosynthetically active radiation (PAR). This study further evaluated and compared the impacts of very strong El Niño and strong La Niña on habitat suitability of O. bartramii. Results showed that habitat modeling method based on SST and PAR could effectively predict the habitat hot spots of O. bartramii in the Norwest Pacific Ocean. It was clearly found that the suitable ranges of SST and PAR varied monthly, and the ranges decreased from September to November. The catch, fishing effort and catch per unit effort (CPUE)tended to linearly increase with the habitat suitability index. Comparing the 2007 year with strong La Niña and the 2015 year with very strong El Niño, it showed that the CPUE and habitat suitability in 2007 were higher than those in 2015. The difference might be attributed to the high enlargement of suitable area of SST and PAR in 2007due to the strong La Niña, while the very strong El Niño in 2015 led to the sharp decrease of suitable area for both SST and PAR. All of these resulted in the low CPUE.