The Indonesian throughflow (ITF) is an ocean current that flows from the Pacific to the Indian Ocean, acting as the upper branch of the global heat conveyor belt. The variability in the ITF has a significant impact on the global climate. The last glacial maximum (LGM), which occurred at ~20 ka, is a benchmark period for the study of paleoenvironment. Here, we investigate the variability of the ITF and the associated change in the carbon cycle during the LGM using a coupled marine physical-biogeochemical model with higher resolution than Earth system models. The preliminary results show that increased sea surface height in the western Pacific strengthens the ITF. Because of the stronger along-coast wind, the upwelling system is also strengthened off the south coast of Java and Sumatra. The nutrient and air-sea CO₂ flux along the ITF and Java-Sumatra upwelling system will be discussed.