Background: Long commuting times have a negative impact on mental health. However, few studies have explored the relationship between commuting time and well-being based on urbanization by region. Our study examines this relationship as well as the effect of regional differences on Korean workers. Methods: We used data from the sixth Korean Working Conditions Survey. Commuting time and occupational factors were assessed using a questionnaire, and subjective well-being was assessed using the World Health Organization-5 Well-Being Index. Regions were divided into the cities and the provinces based on Korea’s administrative divisions. Logistic regression analysis was performed to investigate the association between commuting time and well-being. Adjusted odds ratios (aORs) with 95% confidence intervals (CIs) for well-being were estimated, using participants commuting time of < 20 minutes as a reference group. Results: The total number of workers was 29,458 (13,855 men, 15,603 women). We found higher aORs for low well-being among workers with long commuting times (aOR, 1.23; 95% CI, 1.11–1.36 and aOR, 1.28; 95% CI, 1.16–1.42 for 60–79 and ≥ 80 minutes, respectively). When stratified by sex and region, higher aORs for low well-being were found only in the workers who lived in cities. Conclusion: Long commuting time was negatively associated with well-being in Korean wage workers living in the cities. Policies for reducing commuting time should be discussed to address the mental health of workers, especially those living in metropolitan cities.