Indonesia is passed by an atmospheric phenomenon, called the Madden-Julian Oscillation (MJO), which has an impact on the wave height in the Indonesian Seas. The significant wave height is simulated using WAVEWATCH-III (WW3) numerical model in Indonesian region (90 °E-150 °E, 20 °N-20 °S) forced by surface winds from Cross-Calibrated Multi-Platform (CCMP), Navy Global Environmental Model (NAVGEM), and Navy Operational Global Atmospheric Prediction System (NOGAPS). This simulation is concentrated on MJO phase 3, 4, and 5 which passed through Indonesia and its adjacent waters that occurred in particular time between 1990-2015. In this study, the impact of MJO was analyzed during every monsoon season. In addition, wind speed analysis was carried out to further enrich the analysis of the MJO impact. The simulation result shows that MJO exerts the highest impact during phase 5 and DJF, which contributes to the increase of wind speed (WS) and significant wave height (SWH) in Indonesian inner seas by 6 m/s and 30 cm, respectively, and in southern Lesser Sunda Island by 8 m/s and 1.2 m, respectively. MJO can also contribute to decreasing of the WS and SWH, when it occurred during DJF and MAM phase 3, and JJA phase 4. There is no noticabe change of WS and SWH during SON.
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