The skipjack tuna (Katsuwonus pelamis) is an important fishery resource worldwide, but particularly in the western and central Pacific Ocean. Under the influence of global warming and climate change, the catch potential and the use of this resource directly affect the marine ecosystem, as well as the global economy and food security. Relatedly, investigating the characteristics of future changes in species resources could lead to improved understanding and possibly reduce any negative impacts. The relationships between skipjack abundance and primary productivity on different El Niño events have been confirmed through the catch potential model established. However, the impact of climate change and warming on resources remains unknown. In this study, we demonstrated primary productivity and skipjack catch potential through scenario simulations, and compared the future impacts due to different types of El Niño events, in order to examine the trends of future resource abundance. The results showed that future changes in catch potential and primary productivity with spatial differences are evident. When skipjacks relocate due to environmental changes, the ecosystem might be stressed beyond its limits. Compared to situations involving minor warming, those with continuously intensifying warming result in the increased vulnerability of skipjack fishery resources to the El Niño phenomenon, as well as decreased catch potential. To mitigate potential damage from climate change, we should control and reduce greenhouse gas emissions, which could improve the sustainability and use of skipjack resources by the Pacific island countries in the western and central Pacific Ocean.