Based on the repeated observation of Expendable Bathythermograph (XBT) section dataset, the combined effects of Pacific Decadal Oscillation (PDO) and El Niño-Southern Oscillation (ENSO) events on geostrophic transport of Indone sian throughflow (ITF) are qualitatively and quantitatively understood in this study. The warm PDO phase corresponds to more El Niño (EN) events, and cold PDO phase corresponds to more La Niña (LN) events. The results show that: (1) during the warm PDO phase, the removal of the IOD signal shortens the optimal lag between ITF and ENSO from 7 to 8 to 3–7 months. In contrast, the removal of the IOD influence results in little change in the correlation during the cold PDO phase. The IOD exerts a stronger control over the ITF transport during warm PDO phase. (2) Whatever warm or cold PDO phases, the ITF consistently weakened (strengthened) by ~ 3 Sv (2–4 Sv; 1 Sv = 106 m3 s− 1) approximately 7–9 months (5–7 months) after the EN (LN) events occurrence. However, the most pronounced differences exist during the summer and autumn seasons preceding the onset of EN (LN) events. That is, the weakening of ITF transport in warm PDO phase shifts to strengthening in cold PDO phase. (3) Moreover, this shifts can mainly be attributed by the sum of South Equatorial Current (SEC) and South Java Current (SJC).