The Miocene epoch, marked by significant tectonic and climatic shifts, presents a unique period to study the evolution of South Asian summer monsoon (SASM) dynamics. Previous studies have shown conflicting evidence: wind proxies from the western Arabian Sea suggest a weaker Somali Jet during the Middle Miocene compared to the Late Miocene, while rain-related records indicate increased SASM rainfall. This apparent decoupling of monsoonal winds and rainfall has challenged our understanding of SASM variability. Here, using the fully coupled EC-Earth3 model, we identify a key driver of this decoupling: changes in African topography rather than other external forcings such as CO2 change. Our simulations reveal that changes in Miocene African topography weakened the cross-equatorial Somali Jet and reduced upwelling in the western Arabian Sea, while simultaneously enhancing monsoonal rainfall by inducing atmospheric circulation anomalies over the Arabian Sea. The weakened Somali Jet fostered a positive Indian Ocean Dipole-like warming pattern, further amplifying the monsoonal rainfall through ocean-atmosphere feedbacks. In contrast, CO2 forcing enhances both Somali Jet and rainfall simultaneously, showing no decoupling effect. These findings reconcile the discrepancies between wind and rainfall proxies and highlight the critical role of African topography in shaping the multi-stage evolution of the SASM system.