In this study, catch and effort data of southern bluefin tuna (SBT) from Taiwan longliners operating in the Central Indian Ocean (CIO) during 1982 to 2003 were compiled and their catch per unit effort (CPUE) was standardized using the generalized linear model (GLM). The GLM includes factors such as year, season, by-catch, latitude, sea surface temperature (SST) and the interactive effects among factors. The standardized CPUE and its relationship with SST fluctuation were then analyzed to understand the effects of fishing ground SST variations on CPUE of SBT, as well as their connection to El Niño–Southern Oscillation (ENSO) events. The standardized CPUE in the CIO seemed to oscillate with the sea surface temperature anomalies (SSTA) between 30 and 50°S where SSTA fluctuations were prolonged and slower than the ENSO cycle. It is then very likely that fishing conditions at the CIO fishing ground were influenced by the expansion of the cold water mass from the Southern Ocean, and the colder SST is beneficial to increasing SBT catch rate.