Previous studies indicate significant intraseasonal (20-90 days) variability on the Indonesian Throughflow (ITF) transport produced by the Madden-Julian Oscillation (MJO). These studies, however, mostly focus on the transport through each individual strait, especially Makassar strait, and overall impacts of the MJO on ITF transport are not well understood. This study examines the intraseasonal variability of ITF transport associated with the MJO, including the transport through multiple major straits (Makassar, Lombok, Ombai, Timor) in the Indonesian Seas using a new 1/12° global HYbrid Coordinate Ocean Model (HYCOM) reanalysis. The composite analyses of oceanic and atmospheric variables are performed for the period January 2004-December 2015, in which eighteen well-defined MJO events were identified. Consistent with previous studies, large intraseasonal variability of the Makassar Strait Throughflow is identified from the analysis. In addition, the contribution of anomalous ITF transport through other straits during both active and suppressed phase of the MJO for the total transport is quantified based on the composite analysis.