The vertical habitat of tuna has significant effects on the longline catch rates, which are primarily influenced by oceanographic features. In order to support longline operations and fishery management, several key environmental factors were used to evaluate the influence of vertical habitat on longline catch rates in the tropical Atlantic Ocean. Regression model was used to determine the relationship between environment and longline catch rates, expressed as catch per unit fishing effort (CPUE), while generalized additive model (GAM) was used to evaluate the significance of environmental factors on CPUE. The results revealed that the environment and spatio-temporal factors had significant effects on catch rates, and the relationships were nonlinear. High catch rates were achieved in the summer and winter to the north of the equator, between 30°-50°W. The shape of the 12℃ isolines (open para curves) showed influences on longline catch rates. High catch rates were observed where the depth was lower than 250 m. The hooking rates declined as the depth of 12℃ isolines increased to 400 m. The nonlinear effects of the low depths of thermoclines and relative depths were both like a dome. The longline catch rates increased as the thermocline depth and relative depth increased to 200 m, while at depths greater than 200 m, the catch rates decreased. There were strong relationships between longline catch rates and the thermocline depth and relative depth, which were 200 m and 50 m, respectively. These results suggest that the influences of 12℃ isolines and thermoclines were cross. The catch rates reached maximum levels when the vertical habitat was compressed consistent with hooking depth and decreased when the vertical habitat depth was too large or too small, but could change by adjusting the depth of hooks. The vertical habitat of tuna should be taken into account in fisheries stock assessments and fishing grounds analyses.