The western and central Pacific Ocean (WCPO) is the largest skipjack tuna Katsuwonus pelamis fishing ground in the world. Understanding the spatial–temporal variation of primary productivity in the WCPO is critical, as such variation might be associated with the distribution of skipjack tuna stocks. This study adopts three types of remote sensing data, i.e., sea surface temperature (SST), chlorophyll-a concentration and photosynthetically active radiation, and applies a vertically generalized production model to simulate the euphotic depth-integrated primary productivity (IPP) of the WCPO to elucidate the relationships between the distribution and variation in IPP and the estimated population dynamics of skipjack tuna. In addition, catch data from a Taiwanese purse seine fishing company (2003–2010) were analyzed to improve the accuracy of the model. The results suggest that (a) in the WCPO, the most of the high-IPP locations are in the eastern Pacific areas; (b) the areas in which IPP is significantly correlated with the El Niño Southern Oscillation are mainly located along the equatorial zone; and (c) there were high recruitments of skipjack in 26 and 49 months following an IPP bloom, respectively. The findings from this study reveal the correlation between primary productivity and fish resources and highlight the influence of climate variability on tuna resources.