Abstract: Climate change, particularly extreme climate events, is likely to alter the population connectivity in diverse taxa. While the population connectivity for highly migratory species is expected to be vulnerable to climate change, the complex migration patterns has made the measurement difficult and studies rare. However, otolith biogeochemistry provides the possibility to evaluate these climate-induced impacts. Japanese Spanish mackerel Scomberomorus niphonius is a highly migratory fish that is widely distributed in the northwest Pacific. Otoliths biogeochemistry of age-1 spawning or spent individuals from three consecutive years (2016–2018), during which a very strong El Niño was experienced (2015–2016), were analyzed to evaluate the temporal variation of connectivity for S. niphonius population along the coast of China. The elemental concentrations of the whole otolith showed that Ba: Ca and Mg: Ca values were found to significantly increase in the El Niño year. The random forest classification and clustering analysis indicated a large-scale connectivity between East China Sea and the Yellow Sea in the El Niño year whereas the local S. niphonius assemblages in different spawning areas were more self-sustaining after the El Niño year. These findings lead to the hypothesis that environmental conditions associated with the El Niño Southern Oscillation (ENSO) events in the Northern Pacific Ocean would likely influence the population connectivity of S. niphonius. If so, extreme climate events can result in profound changes in the extent, pattern and connectivity of migratory fish populations. Our study demonstrates that otolith biogeochemistry could provide insight towards revealing how fish population response to extreme climate events.