An eddy-permitting quasi-global oceanic GCM was driven by wind stresses from reanalysis data for the period of 1958–2001 to get the time series of the upper circulation in the Indonesian Sea. The model represents a reasonable pathway of Indonesian Throughflow (ITF) with Makassar Strait making the major passage transfer the North Pacific water southward. The simulated annual mean ITF transport is 14.5 Sv, with 13.2 Sv in the upper 700 m. Annual cycle is the dominant signal for the seasonal climatology of the upper layer transport. Both the annual mean and seasonal cycle agree well with the observation. The overall correlation between the interannual anomaly of the ITF transport and Nino 3.4 index reaches -0.65 in the simulation, which indicates that ENSO-related interannual variability in the Pacific is dominant in controlling the ITF transport. The relationship between the interannual anomalies of ITF and sea surface temperature in the Pacific, the Indian Ocean is not fixed in the simulation. In 1994, for instance, the intensive Indian Ocean sea surface temperature anomaly plays a dominant role in the formation of an impressive large transport of ITF.