Objective: To analyze physical fitness and health status and gender differences of middle school students among 5 minorities (Mongolian, Hui, Uyghur, Zhuang and Korean), and to provide the theoretical basis for the strategy formulation. Methods: The present data came from 3 waves of Chinese National Survey on Students Constitution and Health (2010, 2014, and 2019). According to National Standards for Students Physical Health (2014 Revision), excellent, and excellent good physical fitness and health status were defined. Cochran Armitage test was used to examine the trends of physical fitness and health status. Chi square test and Logistic regression were used to analyze the difference of physical fitness and health status by sex and survey year. Results: From 2010 to 2019, the excellent physical fitness and health status rate of Mongolian, Hui, Uyghur, Zhuang and Korean students increased from 1.8%, 0.7%, 0.3%, 0.5% and 1.3% to 4.3%, 2.8%, 1.2%, 1.3% and 3.5%, respectively. The excellent good physical fitness and health status rate of Mongolian, Hui, Uyghur and Zhuang students increased from 12.9%, 8.0%, 7.2 % and 8.4% to 24.7%, 20.1%, 12.6% and 19.8%( Z =6.15，6.71，4.12，3.06，5.26；11.88，13.42，6.70，11.08， P <0.05), respectively. In 2019, students aged 13 to 15 years showed higher proportion of excellent/excellent good physical fitness and health status than that of students aged 16 to 18. Boys were more likely to be in excellent/excellent good physical fitness and health status than girls from 2010 to 2019. The sex difference in excellent/excellent good physical fitness and health status narrowed during 2010 and 2019. Conclusion Physical fitness and health status of minority students improved while sex difference narrowed during last decade, but there is still a long way to reach the goal proposed by China. Targeted intervention should be proposed to promote physical fitness and health status in accordance with the developmental characteristics, especially for girls and students aged 16 to 18 years.