The foraging depth of yellowfin tuna (Thunnus obesus), which is primarily influenced by the vertical structure of the water temperature, has a significant effect on longline catch rates. Therefore, the generalized additive model (GAM) was applied to analyse the influence of subsurface environmental variables on the longline catch per unit of effort (CPUE) in the central and western Pacific. The results show that subsurface environmental factors have significant impacts on the spatial distribution of yellowfin tuna catches in longline fisheries. The longline CPUE for the yellowfin tuna in the tropical central and western Pacific rise rapidly after 2012. A high catch rate appears in the northern hemisphere during summer in the region near 10°S, 140°E. The upper boundary temperature and depth of the thermocline, the lower depth of the thermocline, the depth of the isotherm at 18℃, and the relative depth between △8℃ and the lower depth of thermocline greatly influence the longline fishing rate. These key environmental factors affect the tropical central and western Pacific yellowfin tuna longline catch. The CPUE increases as the temperature and the depth of the upper boundary of the thermocline increased. The strongly associated relationships between the upper boundary temperature and depth with CPUE were 27−28℃ and 70−90 m, respectively. High catch rates are observed when the lower boundary depth of the thermocline is from 250 m to 280 m. Then, as the lower boundary depth increased, the CPUE value quickly decreased. The effect of the 18℃ isotherm depth on the CPUE of longline fishing initially fluctuated and then increased. The nonlinear effects of the relative depth between △8℃ and the lower depth of the thermocline first decreased and then increased slowly. The strong associations between CPUE and the 18℃ isotherm depths and relative depth are at 230 m and 70 m, respectively. The catch rates reaches a maximum when the vertical habitat is compressed, making it consistent with hooking depth. The catch rates could be changed by adjusting the depth of hooks. The vertical habitat of tuna should be taken into account in fisheries stock assessments and fishing grounds analysis.