As one of the deepest basins over the Indonesian Seas, the Banda Sea is strongly involved in the thermohaline circulation component of the Indonesian Throughflow (ITF). Here, a shift of transport stratification in the Banda Sea has been found between depths of ~500 to 2700 m, with the vertical pattern of the transport changed from a two-component vertical structure of southward-northward during 1980 to 1992, to a three-component northward-southward-northward during 1993 to 2000. Therefore, the vertical distribution of the Banda Sea transport was then separated into three layers. To investigate possible reasons for this event, an ideal thermohaline circulation box model has been used to simulate the Banda basin. Extensive simulations are designed to test the model response for different upstream water sources. The results show that except for layer 1, the two deeper layers both show a prolonged effect after the cessation of changes to the input water sources. The results suggests the shift could result from a relatively short-term increase in the water source from the South China Sea or the South Pacific to layer 3, leading to an increase of southward transport. In layer 2, the model produced an increase in water flow to the north and vertically to both upper and lower layers. In the light of these model results, the reanalysis data was examined further – it is consistent with more water from the South Pacific entering the Banda Sea via the Lifamatola Strait in layer 3 during 1993 to 1996.