This study investigates the cross-sectional descriptive characteristics of male shipbuilding workers’ musculoskeletal disorders (MSDs) and factors associated with MSDs in the neck, shoulders, elbows, low back, or knees. From the national compensation data confirmed as MSDs during three years between 2015 and 2017, 985 male workers were analyzed in terms of age, work experience, occupations, company size, and MSD type according to each body region. In the analysis of frequency and severity according to ‘occupation–body region–MSD type’, ‘Electrician/plumber–low back–herniated disc’ (6.9%) was the form of MSDs with the highest frequency among total MSDs, and ‘Crane–neck–herniated disc’ (500.5 days) was the highest mean of sick leave days. The low back MSDs (28.9%) were the highest frequency, followed by shoulders (27.7%) and knees (16.2%). The herniated disc was frequent in the neck and lumbar region, and the mean of sick leave days of the neck herniated disc (402.2 days) was greater than that of the low back herniated disc (321.1 days). While a rupture was frequent in the shoulder or knee region, the mean of sick leave days for shoulder rupture (335.1 days) was greater than that of the knee rupture (318.8 days). In the binary logistic regression analysis, age was positively associated with MSDs in the neck, shoulder, or elbow regions, while the low back MSDs category was not positively associated with age. Large companies with >1000 employees were highly associated with neck MSDs, while small companies with <30 employees were related to the low back MSDs. This study derives the characteristics for frequency and sick leave days of MSDs in the neck, shoulders, elbows, low back, or knees to prioritize MSD prevention information. The results of this study can be used as primary data for establishing MSD prevention policy.