The wind environment in port areas not only affects port planning and layout but also constrains the navigation time window during operations. During the engineering certification process for port construction, typically only monthly and yearly climatic characteristics of hydrological and meteorological conditions, as well as statistical conclusions on the main weather systems causing high winds and waves in the region, can be considered. These data alone cannot represent the wind and wave distribution in specific operational areas. Sometimes, it is necessary to refer to the wind and wave characteristics of the operational waters for specific port operation point selection. In such cases, remote sensing or simulation techniques, such as computational fluid dynamics (CFD), are used to infer the wind and wave distribution characteristics. Taking Shanghai Yangshan Deepwater Port as an example, the design of the pilot boarding point for strong winds and waves is located near the main channel, providing limited protection against high winds and waves. On average, there are 11.9 instances of pilot traffic control caused by high winds and waves each year. To mitigate the impact of severe weather on port operations, it is proposed to move the temporary boarding point for pilots in strong winds and waves westward to the east gate closer to the port area. Traditional hydrological and meteorological statistical data cannot support the selection of the new area, so it was decided to use CFD technology to simulate the wind environment in the relevant island and reef area and analyze the wind field distribution under different wind directions. Combined with the three-year statistical data from the meteorological station on Xiaoyangshan Island, a new area for the temporary pilot boarding point was selected. The CFD wind environment simulation results provided the primary technical support for determining the reference area.