Generally, the air-sea momentum, heat, and CO2 gas flux are calculated in field observation using the eddy correlation method, which simultaneously measures the horizontal and vertical wind components. Measuring the components of wind velocity is usually limited to fixed installations owing to the minor effect of the platform on the wind flow. Occasionally, numerical simulations are sometimes used for shipboard observations. However, the details of the effect of the wind flow around an observation ship are scarcely investigated using numerical simulations, although ships affect the wind flow and wind direction by wind distortion. In this study, we investigated the effect of ships on the wind flow around the Hakuho–Maru of the Japan Agency for Marine-Earth Science and Technology using a numerical simulation. As a result of the flow visualization, measuring the horizontal and vertical components of wind velocity was very difficult because the wind distortion (upward and downward gusts, among others) was very large owing to the effect of the ship. This showed that the effect of the ship was significant for the measurements of air-sea momentum, heat, and CO2 gas flux.