The newly upgrade physics of shallow water effect of the internal structure for third generation ocean-wind wave model MRI-III Shallow Water Mode (WS), was implemented to simulate the wave condition in the region of South China Sea (SCS) during the typhoon season in 2013 (Sonamu 3/1/2013-8/1/2013 and Shanshan 21/2/2013-22/2/2013). The purpose of this study is to evaluate the performance of the Shallow Water Mode (WS) as compared to Deep Water Mode (WD) of the wave model MRI-III in simulating the significant wave height (SWH) characteristic. The JMA MRI-III wave model was simulated using the ECMWF Reanalysis (ERA-Interim) at 1.0-degree resolution 6 hourly 10- meter wind data to simulate the wave condition within the two month period. The SWH from MRI-III WS and WD was compared to the Archiving, Validation and Interpretation of Satellite Oceanographic (AVISO) altimetry data over the 18 location in SCS. The simulation result was also compared to the Layang-Layang buoy (LB) observation that is located in the SCS (about 300 km north-west from Kota Kinabalu). For validation purpose with satellite data, the model result generally tally with the measured values, but there was some underestimation of the model SWH, which was indicated by the negative values of the mean errors at all 18 selected locations. The model was relatively correlated with observation measurement for both WS and WD, as shown by the correlation coefficient (CC) values for 18 different locations, which were between 0.60 and 0.93. Meanwhile, the validation with LB shows that the WS performed well over the WD, for both the coarse grid (CG) and fine grid (FG) resolutions. The model errors for WD for FG resolution are 1.76 (RMSE) and 0.64 (CC), respectively. Meanwhile, WS are compared to the measured buoy data especially for the FG resolution with its RMSE is0.21, and its CC is 0.80, which indicate that the improvement of the MRI-III, WS wave model significantly improves the wave simulation accuracy in SCS region with the newly introduced shallow water effect in the wave evolution calculation.