This study aimed to determine the trends in prevalence of childhood overweight and malnutrition in a large Chinese ethnic minority population from 1991 to 2010. In the Chinese National Survey on Students' Constitution and Health from 1991 to 2010, multistage stratified sampling was conducted in the series of cross-sectional studies. Participants were 7-18-year-old students randomly selected by sex and region, and included Han and 26 ethnic minorities. During the survey period, the overall prevalence of overweight increased from 5.8% to 13.5%, and malnutrition trend increased from 3.6% to 4.1% in ethnic minority children and adolescents. Moreover, Korean and Mongol children were more likely than Han children to be obese (Korean: RR = 1.52; 95% CI: 1.48-1.56; Mongol: RR = 1.24; 95% CI: 1.20-1.28). Among these minorities, the Dongxiang and Li children were more likely to be malnourished (Li: RR = 1.47; 95% CI: 1.37-1.57; Dongxiang: RR = 1.45; 95% CI: 1.34-1.58). Shui, Khalkhas, Lisu, and Monguor children were less likely to be overweight and malnourished compared with the Hans. The prevalence of overweight among ethnicities increased yearly while that for malnutrition has fluctuated over the past few decades.