Oceanic temperature fluctuations are one of the leading factors affecting marine fish populations. Indian Ocean Dipole (IOD), characterized as the sea surface temperature (SST) anomaly change, is an ocean–atmosphere interactive process causing interannual climate variability in the Indian Ocean. Influences of the IOD on the tuna catch rates are supported by previous research. Yet, there remains limited information about the impacts on the abundance of tuna stocks. In this study, we used the standardized Catch Per Unit Effort (CPUE) index to present the stock abundance and compared the effects of the IOD on the bigeye tuna (Thunnus obesus) and yellowfin tuna (Thunnus albacares) among different management areas of the Indian Ocean Tuna Commission (IOTC). Results show significant correlations between IOD events on both species’ abundance in the tropical western Indian Ocean. However, in the tropical eastern Indian Ocean and the southern Indian Ocean, neither bigeye nor yellowfin tuna abundances were significantly correlated by the IOD. For the whole Indian Ocean, IOD was significantly correlated uniquely with the yellowfin tuna abundance. Our results emphasized the importance of evaluating the climate variability effects over fisheries abundance species by species and per fishing areas analyses.