Understanding of the temporal variation of oceanic heat content(OHC) is of fundamental importance to the prediction of climate change and associated global meteorological phenomena. However, OHC characteristics in the Pacific and Indian oceans are not well understood. Based on in situ ocean temperature and salinity profiles mainly from the Argo program, we estimated the upper layer(0–750 m) OHC in the Indo-Pacific Ocean(40°S–40°N, 30°E–80°W). Spatial and temporal variability of OHC and its likely physical mechanisms are also analyzed. Climatic distributions of upper-layer OHC in the Indian and Pacific oceans have a similar saddle pattern in the subtropics, and the highest OHC value was in the northern Arabian Sea. However, OHC variabilities in the two oceans were different. OHC in the Pacific has an east-west see-saw pattern, which does not appear in the Indian Ocean. In the Indian Ocean, the largest change was around 10°S. The most interesting phenomenon is that, there was a long-term shift of OHC in the Indo-Pacific Ocean during 2001–2012. Such variation coincided with modulation of subsurface temperature/salinity. During 2001–2007, there was subsurface cooling(freshening)nearly the entire upper 400 m layer in the western Pacific and warming(salting) in the eastern Pacific. During2008–2012, the thermocline deepened in the western Pacific but shoaled in the east. In the Indian Ocean, there was only cooling(upper 150 m only) and freshening(almost the entire upper 400 m) during 2001–2007. The thermocline deepened during 2008–2012 in the Indian Ocean. Such change appeared from the equator to off the equator and even to the subtropics(about 20°N/S) in the two oceans. This long-term change of subsurface temperature/salinity may have been caused by change of the wind field over the two oceans during 2001–2012, in turn modifying OHC. Understanding of the temporal variation of oceanic heat content (OHC) is of fundamental importance to the prediction of climate change and associated global meteorological phenomena. However, OHC characteristics in the Pacific and Indian oceans are not well understood. Based on in situ ocean temperature and salinity profiles mainly from the Argo program, we estimated the upper layer (0-750 m) OHC in the Indo-Pacific Ocean (40 ° S-40 ° N, 30 ° E-80 ° W). Spatial and temporal variability of OHC and its likely physical mechanisms are also analyzed. Climatic distributions of upper-layer OHC in the Indian and Pacific oceans have a similar saddle pattern in the subtropics, and the highest OHC value was was in the northern Arabian Sea. However, OHC variations in the two OHC in the Pacific has an east-west see-saw pattern, which does not appear in the Indian Ocean. In the Indian Ocean, the largest change was around 10 ° S. The most interesting phenomenon is that, there wasa long-term shift of OHC in the Indo-Pacific Ocean during 2001-2012. Such variation coincided with modulation of subsurface temperature / salinity. During 2001-2007, there was subsurface cooling (freshening) nearly the entire upper 400 m layer in the western Pacific and warming (salting) in the eastern Pacific. During 2008-2012, the thermocline deepened in the western Pacific but shoaled in the east. In the Indian Ocean, there was only cooling (upper 150 m only) and freshening (almost the entire upper 400 m) during 2001-2007. The thermocline deepened during 2008-2012 in the Indian Ocean. Such change was from the equator to off the equator and even to the subtropics (about 20 ° N / S) in the two oceans. long-term change of subsurface temperature / salinity may have been caused by change of the wind field over the two oceans during 2001-2012, in turn modifying OHC.