The Indonesian Archipelago provides important heat transport pathways of the Western Pacific Warm Pool between the northern Indian Ocean and western equatorial Pacific Ocean, that exert important impacts on global climate change. This study investigated AMS 14C, ?18O, planktonic foraminifer assemblages and sedimentation rates in three piston cores collected in the Indonesian Archipelago. The results indicate that changes in the Indonesian Archipelago heat transport pathways were phase characteristic and in steps during the last deglaciation. In the deglaciation Termination IA, at about 12.5 kaBP, sea level rose rapidly in a short time period, and Makassar and Lombok straits widened suddenly for warm and fresh water from the Pacific to pour into the Java Sea and eastern Indian Ocean. During the Termination IB, about 9.5 kaBP, sea level rose rapidly again, and the South China Sea (SCS) started to connect with the Java Sea. With monsoon actions, a large amount of fresh water from the SCS shelf area flew through the Indonesian Archipelago.