On interannual timescales, Southeastern Indian Ocean (SETIO) upwelling is closely related to the Indian Ocean Dipole (IOD) and El-Niño Southern Oscillation (ENSO). IOD events tend to be stronger when they co-occur with ENSO. However, the linkage between SETIO upwelling and IOD asymmetry that is independent and dependent on ENSO phases is not clear. This issue is investigated in this study based on the analysis of Kelvin wave propagation, subsurface ocean dynamics, and thermocline depth, as well as chlorophyll-a concentration as the upwelling parameters. The impact of IOD asymmetry related with ENSO on SETIO upwelling characteristics was assessed based on composite analysis conducted on two positive IOD events co-occurring with El-Niño events (pIOD–EN) ( 1997 and 2015) and three independent positive IOD (pIOD) events (1994, 2006 and 2012).  During pIOD event, easterly wind anomaly generates zonal sea surface height anomaly (SSHA) across the Indian Ocean, followed by upwelling Kelvin waves propagation along the equator to the coast off Sumatra-Java and also damped the Wyrtki Jet. Consequently, in the Southeastern Indian Ocean, the shallow thermocline depth strengthens the SETIO upwelling in this region as well. During pIOD-EN event, equatorial zonal wind anomaly blows longer and stronger, resulting in earlier and more persistent shallowing of the thermocline depth, starting in May until April in the following year, and also stronger upwelling with peak amplitude of up to 2.78 standard deviation. Even though the upwelling is stronger during pIOD–EN event due to shallower thermocline depth, the chlorophyll-a concentration during independent pIOD events is much higher with peak amplitude of up to 3.19 standard deviation. It is suggested that this is the result of widespread cold SST anomaly distribution south of 15°S due to the absence of El Niño.