Godfrey's Island Rule assumes that no vertical flow occurs through the "depth of no motion", but observations indicate that deep upwelling is significant below the wind-driven ocean circulation in the tropical Pacific Ocean. In this study, we revisit the Island Rule in a context of multi-islands and considering the contribution from deep upwelling in the south Pacific Ocean. We solve the momentum equation with the continuity equation containing deep upwelling velocity, and an analytical solution of volume transport through the straits between three islands is derived. The transport of Indonesian Throughflow (ITF) is estimated with this analytical solution using wind stress and vertical velocity from a near-global 1/10° ocean general circulation model. The estimated ITF transport from this deep-upwelling-included multi-island rule is compared with the simulated  "actual"  ITF transport across the 114°E section (8.5°S–22.5°S). The comparison suggests that the ITF transport estimated from the deep-upwelling-included multi-island rule is in well agreement with the "actual"  ITF transport with a correlation coefficient of 0.78 and a mean difference of 0.04 Sv. The correlation with the INSTANT observations  also reached 0.78. These results indicate that it is very necessary to consider deep upwelling when estimating the ITF transport using the Island Rule.