The low-lying coastal and island regions are vulnerable to sea level rise and extreme events. Compounded by marine heatwaves, sea level extremes have devastating impacts on coastal community and marine ecosystems. As long tide gauge records are sparse, sea level extremes around Indonesia are poorly understood, and the Compound Height-Heat EXtreme (C-HHEX) events remain unexplored. Here we combine in situ and satellite observations with model simulations, to investigate the long-lasting (>1 month) sea level extremes and C-HHEXs along Indonesian coasts of the Indian Ocean since the 1960s. We find that 90% (80%) of the extreme sea level (C-HHEX) events, with a maximum monthly sea level anomaly of 0.45m, are clustered in an 8yr period of 2010-2017, due to anthropogenic global sea level rise and decadal enhancement driven by changing surface winds associated with a combined invigoration of the Indian and Pacific Walker Cells, atmospheric overturning circulations in east-west direction. Remote and local surface wind anomalies associated with negative phases of the Indian Ocean Dipole (IOD) - enhanced by La Niña – drive individual C-HHEX events under a precondition of shallow thermocline (a region of subsurface ocean with temperature decreases rapidly downward). By contrast, winds associated with monsoon and its intraseasonal oscillations force the sea level alone events under a deep thermocline condition. We conclude that the shoaling thermocline in eastern Indian Ocean under anthropogenic warming and global sea level rise favorably precondition the ocean for stronger and more frequent sea level extremes and C-HHEXs, increasing the environmental stress on Indonesia.