The Indian Ocean Dipole (IOD) significantly influences tropical precipitation patterns, with its positive phase triggering severe floods and droughts in Indian Ocean rim countries. These climate extremes are projected to intensify under global warming. However, how the IOD will modulate the tropical precipitation and ecosystem response under warming climate remains unknown. Here, we uncover contrasting precipitation response to IOD seasonality and highlight the pivotal role of boreal summer monsoon circulation. An early-onset of the IOD during boreal spring enhances its intensity through non-linear interactions with the summer monsoon circulation, amplifying tropical precipitation responses. Conversely, a late-onset IOD exhibits weaker ocean-atmosphere feedbacks, resulting in reduced amplitude, early decay, and drought-like conditions across the tropics. Enhanced precipitation during early-onset IOD enhances the gross primary productivity over the Asian landmass, which has significant implications for food security in a region that supports the majority of the global population. Meanwhile, marine productivity in the Arabian Sea shows a substantial decline during both early and late IOD events, threatening one of the world's most productive oceanic ecosystems. Using coupled climate model projections, we demonstrate that tropical precipitation is likely to enhance with early-IOD under greenhouse warming. These findings have critical implications for the hydrological cycle, ecosystem and, socio-economic resilience in Indian Ocean rim countries.