In the eastern tropical Indian Ocean, intraseasonal variability (ISV) affects the regional oceanography and marine ecosystems. Mooring and satellite observations documented two periods of unusually weak ISV during the past two decades, associated with suppressed baroclinic instability of the South Equatorial Current. Regression analysis and model simulations suggest that the exceptionally weak ISVs were caused primarily by the extreme El Niño events and modulated to a lesser extent by the Indian Ocean dipole. Additional observations confirm that the circulation balance in the Indo-Pacific Ocean was disrupted during the extreme El Niño events, impacting the Indonesian Throughflow Indian Ocean dynamics. This research provides substantial evidence for large-scale modes modulating ISV and the abnormal Indo-Pacific dynamical connection during extreme climate modes.