We assessed the risk of fatal occupational injuries among migrant workers with two different types of employment permits in South Korea. This observational study used national data from January 2007 to September 2018 and analyzed 42,089 cases of occupationally injured migrant workers of Chinese nationality. Fatality rates were analyzed according to year, sex, age, occupation, industry, and type of employment permit. Chinese workers were permitted to work for one employer and prohibited from changing employers, whereas Korean-Chinese workers were permitted to change their employer. The adjusted fatality rate of occupational injuries of Chinese migrant workers was significantly higher (1.80-fold, 95% confidence interval 1.31-2.46) than that of Korean-Chinese migrant workers. The prohibition on changing workplaces; male sex; age ≥ 45 years; machine operator; construction industry; and agriculture, livestock, and fisheries industry were risk factors for fatal occupational injuries. The results imply a need for revision of the migrant-worker employment permit systems and implementation of occupational safety and health policies for all workers to promote health equity.