The stratospheric impact of the sea surface temperature (SST) variability in the Indian Ocean has attracted extensive attention. Recent warming of the tropical Indian Ocean is characterized by increases in both the magnitude and zonal gradient, which is related to the variability in the positive phase of the Indian Ocean basin mode (IOBM) and Indian Ocean dipole mode (IOD). Yet, previous studies mainly focused on the stratospheric impact of the IOBM. Using the Whole Atmosphere Community Climate Model (version 4), this study explores the impact of positive IOD events on the stratosphere and compares it with the IOBM. Results show that the IOBM (IOD) serves to dry (moisten) the tropical lower stratosphere on the annual average. The moistening (drying) of the lower stratosphere in response to IOBM occurs mainly in winter and spring (autumn), while the IOD exerts a moistening effect in winter. Both modes can enhance the northern stratospheric polar vortex, and the effect of IOD is close to that of IOBM, although SST anomalies associated with the IOD are smaller. This implies that the Indian Ocean SST gradient exerts a greater influence on the Northern Hemisphere stratosphere than does the Indian Ocean SST magnitude. Moreover, both modes weaken the southern stratospheric polar vortex, but the effect of IOD is much smaller since its impact on stationary waves is weak. Contrary to the Northern Hemisphere stratosphere, the Southern Hemisphere stratosphere is more sensitive to the Indian Ocean SST magnitude than to the SST gradient.