Indonesian throughflow (ITF) regions are important in terms of inter-oceanic exchange of heat as well as freshwater between the Pacific Ocean and the Indian Ocean. These regions also linking the North Pacific Ocean and North Atlantic through a global conveyor belt. However, information about the long-term variations of sea surface temperature (SST) across the ITF regions is rather limited. Here, we use long-term Hadley sea surface temperature and advance satellite-derived sea-surface winds to understand long-term changes in and around the ITF. The SST has been lower during the summer season (May–August) with a pronounced minimum in the eastern Indonesia region (INA) and then decreases towards the west due to the activity of southeasterly monsoon winds. The cooling is noticed in the beginning of May, intensifies during July and subsides during the later half of August. The Lambok Strait has been identified as the coolest region (<26°C) in the ITF. Though there has been a general agreement of warm and cool SSTs with El Niño and La Niña conditions respectively, and increasing trend since 1970s, however, there is no consensus among the major passages in the ITF, suggesting complex internal dynamic processes those need to be studied.