While the prevalence of musculoskeletal disorders has recently increased among Korean workers employed in highly physically and psychologically demanding jobs, the relation among these domains remains relatively unexplored. We examined 2,037 subway workers in Seoul, that collected data via questionnaire survey on musculoskeletal symptoms and the work environment, administered in 2009, 2012, and 2015. Generalized estimating equation (GEE) analysis was used for statistical analysis. After conducting GEE analysis by adjusting for the sociodemographic and occupational characteristics, we found the prevalence of musculoskeletal symptoms significantly increased in cases with high Depression, Anxiety and Stress Scales (DASS) scores compared with low DASS scores, especially on shift workers. An integrated management method that considers ergonomic and mental health factors, should be used to better manage musculoskeletal symptoms in subway workers.