This study was conducted to determine whether the layout of wheelhouse and work environment of coastal improved stow net fishing boats affect the physical abnormalities of wheelhouse workers through a survey and to use it as basic data to improve the wheelhouse work environment. The analysis results are as follows. The result of factor analysis on the wheelhouse work environment was classified into three factors: suitability of work environment, suitability of work space arrangement, and layout of navigational and fishing equipment. The result of factor analysis on physical abnormalities was divided into two factors: physical pain and fatigue. The results of regression model analysis showing factors affecting physical pain showed that the t-value in the regression model was 3.625 (p < 0.05), indicating that the work environment suitability had an effect on the physical pain. Work environment suitability had a significantly positive effect on the physical pain. As work environment suitability increased by 1, the physical pain increased by 0.371 (p < 0.05). The results of regression model analysis showing the influencing factors on fatigue were found to have a t-value of 3.009 (p < 0.05) in the regression model, indicating that the work environment suitability had a significantly positive effect on the feeling of fatigue. It was found that fatigue increased by 0.324 (p < 0.05) as the work environment suitability increased by 1. In addition, the manageability of task suitability was found to be t = –2.521 (p > 0.05). As the manageability of task suitability increased, the skipper’s fatigue level decreased. From these results, it is inferred that the wheelhouse of the current coastal improved stow net fishing boats causes physical pain and fatigue for the skippers. In order to reduce such physical pain and fatigue, and to improve safe fishing operation and job satisfaction, it is necessary to provide a wheelhouse to fishermen on coastal improved stow net fishing boats in consideration of the characteristics of the wheelhouse work of fishing boats and in consideration of users.