Oceanic mesoscale eddies are pivotal in redistributing mass and heat. Despite a warming-induced increase in global oceanic stratification, previous studies have reported a global increase in mesoscale eddy activity, particularly in eddy-rich regions, pointing to a complex and regionally contingent response to climate change. Here we show that the eddy kinetic energy (EKE) over the two wings of the tropical Indo-Pacific Ocean shows an opposite trend over the past three decades, with a pronounced decreasing in the western tropical Pacific Ocean (WTPO) but a significant increasing in the southeastern tropical Indian Ocean (SETIO). We find that the EKE decline in the WTPO is mainly due to weakened intra-seasonal wind work, while the EKE increasing in SETIO is mainly driven by weakened stratification in the north and enhanced shear in the south, both of which are associated with the intensified Indonesian Throughflow.