SignificanceMainland Southeast Asia is a densely populated region largely devoid of long paleoclimate records. Here, we use a stalagmite from Vietnam to reconstruct Southeast Asian autumn monsoon rainfall variability over the last 45,000 y. We show that sea level, specifically the inundation history of the Gulf of Tonkin and South China Shelf, drove substantial changes in local rainfall. Additionally, we find that autumn rainfall responds to millennial-scale changes of the Atlantic Meridional Overturning Circulation. These findings reveal the considerable variability of the Southeast Asian autumn monsoon, including a propensity for abrupt change. Finally, agreement between our stalagmite record and climate model simulations demonstrates that models correctly capture the main drivers of Southeast Asian autumn monsoon rainfall on millennial-orbital timescales.