The analysis of ocean surface waves is essential to ensure safe navigation. Since 2010, different on-board observation data from bulk carriers, including those navigating high-risk shipping regions in the southern hemisphere with strong ocean currents, have been collected for 6 years. High-resolution numerical simulations of ocean waves for four rough sea cases, considering the effect of wave-current interaction on ship navigation, have been performed using the WAVEWATCH III model. The simulations considered the ocean surface wind force from the widely used reanalysis database of the National Centers for Environmental Prediction Final and European Center for Medium-range Weather Forecasts Interim Reanalysis. To provide practical suggestions for safe navigation by avoiding possible high-risk ocean regions and construct a more effective and efficient optimum ship routing system, the model results were validated based on on-board observations, followed by discussions on the responses of ship motion and navigation to sea states at different levels. Finally, early warning criteria, including various operational ocean parameters for ballast and loaded ships sailing in rough seas were identified.