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Significant Wave Height (SWH) in Natuna Waters has been simulated during Typhoon Hagibis event in the period of 20th – 27th November 2007 in the South China Sea by using Simulating WAve Nearshore (SWAN) model with 1/24° spatial resolution. 1/4° wind data obtained from Cross-Calibrated Multi-Platform (CCMP) and 1/120° bathymetry data derived from General Bathymetry Chart of the Ocean (GEBCO) are used as model input. Open boundary values for the SWAN simulation are obtained from WAVE WATCH III (WW3) results, which are provided by Indonesian Geospatial Information Agency (BIG). The model results show that swell generated by Typhoon Hagibis arrived in the Natuna Waters after 3-day travel time, which is 23rd November 2007. Typhoon Hagibis has an impact on swell propagation from the South Cina Sea to the Natuna Waters. SWH in the Natuna Waters during the peak phase of Typhoon Hagibis and Mitag (23rd November 2007) vary between 0.8 – 3.5 m. There are 6 observation points in the study area to investigate SWH variation from 22nd October – 22nd December 2007. Point 1 (P1), Point 3 (P3) and Point 5 (P5) show points in the northern part of the Natuna island, Subi Besar Islands and Riau Islands, respectively. Meanwhile, Point 2 (P2), Point 4 (P4) and Point 6 (P6) show points in the southern part of the Natuna island, Subi Besar Islands and Riau Islands, respectively. Typhoon Hagibis in the peak phase generates the SWH at P1, P3, and P5 of about 0.6 – 2.5 m and generates the SWH at P2, P4, and P6 of about 0. 5 – 1.6 m.