The skipjack tuna (Katsuwonus pelamis) is a highly migratory pelagic species that is abundant in tropical and temperate seas. In this study, skipjack tuna marked with archival tags were released near Green Island in southeastern Taiwan in order to examine changes in their body temperature as they moved through their natural environments. Five fish were recovered, depths occupied ranged from 0 to 310 meters, ambient temperature ranged from 13.1℃ to 28.3℃ and peritoneal cavity temperature ranged from 17.0℃ to 28.2℃, and diving patterns correlated with diurnal cycles. The heat budget model revealed physiological and behavioral thermoregulation in which peritoneal temperatures were maintained above ambient; this was particularly evident during daytime deeper dives. As skipjack tuna ascends to the surface, the average heat-transfer coefficient is 2.7 ± 0.6 (10-3/s), whereas when they return, the average heat-transfer coefficient is 0.9 ± 0.3 (10-3/s), indicating that body heat is retained. When fish dives below the mixed layer depth, the ambient temperature drops rapidly with the depth, while peritoneal cavity temperature descent slowly at a rate of about 7 minutes after the dive. Using our model, we were able to estimate peritoneal temperatures based on the ambient water temperature. According to our findings, skipjack bonito regulates thermoregulation by altering heat transfer coefficients via a physiological mechanism. This mechanism and behavior are comparable to those of species of Thunnus. In conclusion, skipjack tuna can cross the thermocline or expand its cruising range in cooler water in order to find or utilize additional resources more broadly.