With the highest sea surface temperature in the modern world, the Western Pacific Warm Pool (WPWP) is the thermal dynamo for global atmospheric circulation which greatly influences ocean circulation in the tropical Pacific. The closure of the Indonesian Seaway provided the tectonic background for the formation of the WPWP during the late Cenozoic. Five land barriers are identified within the region and served as blockages to Indonesian through-flow. Based on the history of the evolution of these barriers, a two-closure model for the Indonesian Seaway is proposed. While the closures of the Indonesian Seaway facilitated the formation of the WPWP, the related northward movement of the Australian Plate was not favorable for the formation of the WPWP, as it blocked the flow of tropical warm water from the Pacific. Thus the evolution of the WPWP is a combined product of these positive and negative effects of plate tectonic movement. The history of the WPWP can be divided into the following stages: The proto-WPWP was formed during 11-9 Ma. 9-6 Ma was the period when the WPWP experienced its first waning. The formation and evolution of the modern WPWP occurred since 6 Ma. 1-0.2 Ma was the period when the WPWP experienced its second waning. This scheme of the evolution of the WPWP is preliminarily validated by paleo-oceanographic data from ODP Site 1143.