The Indonesian Throughflow (ITF), as the only oceanic connection between the tropical Pacific and Indian Oceans, significantly influences the ocean heat distribution and Indo‐Pacific climate system. Using the Connectivity Modeling System particle tracking method and GLORYS reanalysis data, we find that the

spreading of ITF water after entering the eastern Indian Ocean is strongly altered by extreme Indian Ocean Dipole (IOD) events. The ITF water spreads more southward during extreme negative IOD (nIOD) events and northward with increased westward transport during extreme positive IOD (pIOD) events. The meridional

displacement is approximately 0.5◦ of latitude relative to the climatological mean. These variations are primarily driven by direct wind stress forcing and sea surface height (SSH) gradients induced by the wind stress curl and Ekman pumping. Compared with moderate IOD events, the impact of extreme IOD events on ITF

spreading is more pronounced since extreme IOD events are typically characterized by stronger anomaliesin the eastern Indian Ocean. The IOD induced ITF shifts significantly alter heat transport in the southeastern tropical Indian, and also modulate the Leeuwin Current (LC), enhancing it during nIOD and weakening it during pIOD events. Furthermore, the changes in the ITF significantly modulate the LC heat transport and play an important role in regulating the occurrence of Ningaloo Niño events along the western coast of Australia.