Anomalous sea temperature changes could have direct impacts on fish spatial distribution and stock dynamics. Large-scale climate fluctuations as one of the major reasons causing temperature changes has attracted extensive attention. However Indian Ocean Dipole (IOD), an ocean-atmosphere interaction causing interannual climate variability, has not been largely explored. And few of studies tested whether IOD have different effects between different tuna species and whether IOD have spatially distinct influences on one single tuna species. This study adopted public longline fishery data and spatial structure carried by IOTC comparing the differences of IOD impacts between bigeye tuna and yellowfin tuna. Results found that IOD event have significant influence on bigeye tuna only in the tropical western Indian Ocean. For yellowfin tuna, IOD showed significant effects on catch per unit effort (CPUE) both in tropical western and eastern Indian Ocean. And indicators showed that IOD have more significant influence on yellowfin tuna than bigeye tuna. In the south Indian Ocean, both for bigeye tuna and yellowfin tuna, IOD didn’t show obvious relationship with CPUE.