Skipjack tuna (Katsuwonus pelamis) is an important resource for purse seine fishing in the Western and Central Pacific Ocean. In order to explore the spatial and temporal differences in the impact of environmental factors on the fishing rate of skipjack tuna, this paper evaluates the fishing logbook data of tuna purse seine fishing vessels in the Western and Central Pacific Ocean from 2009 to 2018 in mainland China, as well as the corresponding marine environmental data. Exploratory regression analysis, spatial autocorrelation analysis, and the geographically weighted regression (GWR) model are used to explore the spatial and temporal heterogeneity of standardized environmental factors and the fishing rate of skipjack tuna. The results show that: (1) The fishing rate of skipjack tuna has spatial aggregation. In terms of space, there are 2–3 main aggregation areas, which are concentrated in 152°–164°E, 3°N–7°S sea area on the west side, 164°–175°E, 5°N–4°S sea area on the east side, and 175°–180°E sea area in the second quarter. In terms of time, the degree of aggregation had values of fourth quarter＞first quarter＞second quarter. (2) The spatial heterogeneity degree of the effects of environmental factors on the fishing rate of skipjack tuna had values of sea level anomaly (SLA)＞mixed layer depth (MLD)＞net primary production (NPP)＞sea surface temperature gradient (SSTG). (3) SLA and MLD had significant negative effects on the fishing rate of skipjack tuna because the corresponding values of SLA and MLD were smaller in the surface nutrient-rich areas. NPP and SSTG were mainly positively affected because the frontal where the cold and warm water intersects is greatly affected by these two factors. (4) The GWR model was tested, and it was found that its residuals showed smaller spatial autocorrelation, indicating that the GWR model has a better fitting effect and is better than the ordinary least squares (OLS) method.