Tropical cyclone Cempaka entered South Java sea from 25th November 2017 until 27th November 2017 and caused strong winds and high waves. Delft 3D Modeling Simulation was used to investigate the effect of tropical cyclone Cempaka development on sea level rise in coastal areas and high waves in the South Java sea. The FNL wind data with a resolution of 0.25° × 0.25 ° and GEBCO bathymetry data with a grid resolution of 30 seconds was used as input to the Delft 3D model. The results of the study showed that there was an increase of significant wave height during the tropical cyclone Cempaka period with significant wave values from 1 to 3.5 meters on 27th November 2017. While for the value of sea level height in the coastal area showed results there was an increase during cyclone Cempaka period with anomalies values to 0.4. However, at the center of the cyclone had a low anomaly value that reached -0.2. From the results of the correlation test and RMSE test on sea level Delft 3D output obtained a correlation value of 0.85 and error 0.43 in the Sadeng, Yogyakarta. while the correlation test and RMSE test for the significant wave height parameter obtained a correlation value -0.198 and error value 0.168.