The Madden-Julian Oscillation (MJO) exhibits evident interannual variations, which have been mostly attributed to modulations of El Niño-Southern Oscillation (ENSO) in previous studies. However, whether the basin-wide warming/cooling of the Indian Ocean (IO) independent of ENSO could affect the MJO remains elusive. Here, we show that the MJO tends to initiate more westward and only propagate confined over the IO under warm conditions during boreal summer. In contrast, a cold IO results in an eastward-shifted MJO initiation and smooth propagation across the Maritime Continent (MC)-western Pacific (WP). The genesis location is mainly associated with warm ocean beneath the MJO, which accumulate more during warm conditions. Additionally, the warming of the IO induces anomalous anticyclone and stronger vertical wind shears over the WP, which synergistically lead to stronger Rossby wave while weaker Kelvin wave components, thereby inhibiting the MJO eastward propagation. Moreover, the suppressed convection and thus low-level Kelvin easterly wind anomalies over the MC-WP region become weaker with the warming of the entire IO. Consequently, the premoistening dominated by the high-frequency synoptic-scale meridional advection decreases and causes nonpropagating MJO during boreal summer. These findings highlight that interannual variations of the MJO could be attributed by considering independent modulation effects of the IO.