Using eddy-resolving numerical simulation data and historical hydrological observation data, this study investigates the sources, seasonal and interannual variability of two subsurface undercurrents under the Indonesian Throughflow—the Ombai Undercurrent located in the Ombai Strait and the Timor Undercurrent located in the Timor Channel. The results indicate that these two undercurrents exist at depths of approximately 200-800 m, which are a quasi-permanent undercurrent system. The formation of the Ombai Undercurrent is mainly related to the eastward extension of the South Java Undercurrent, while the water source of the Timor Undercurrent is more complex, mostly a mixture of the South Java Undercurrent and the Leeuwin Undercurrent. Both subsurface undercurrents exhibit significant seasonal and interannual variations, with a significant semiannual period at the seasonal scale, typically peaking during the Indian Ocean monsoon transition period (April, May, and October). Combining historical wind, satellite altimeters, and temperature and salinity observation data, it is found that the meridional pressure gradient in the subsurface layer related to local wind and their upwelling is the dominant factor leading to their seasonal changes. At the interannual scale, there is a period of 2-4 years for subsurface undercurrents, which is significantly correlated with the Indian Ocean dipole.