To investigate the effect of two-year nutritional intervention on the body composition in Yao primary school students in Guangxi Zhuang Autonomous Region.Four primary schools in towns mainly inhabited by Yao People in Jinxiu Yao Autonomous County of Guangxi Zhuang Autonomous Region were chosen randomly as the intervention schools, from which one class was randomly chosen per grade from grades 2-4(7-12 years old); Four other primary schools with similar economic and social conditions to the intervention schools were chosen as the control schools. In total, 190 and 146 students were included in the intervention group and the control group, respectively. The control group gave basic food allowance and the intervention group gave milk and eggs on this basic. Students in the intervention group were subject to nutritional intervention. The change in body composition of students of different body weights was observed and analyzed at the baseline time(September 2015; T0), and 1(T1) and 2(T2) years after intervention. The mixed linear model was used to analyze repeated measures data, and multivariate ANOVA was performed.No significant differences existed in all indexes for both boys and girls between the two groups at T0(P > 0.05). At T1 and T2, as compared with the control group, the fat-free body weight(χ~2=7.253, P<0.05), body fat(χ~2=6.181, P<0.05; χ~2=5.226, P<0.05) and body fat percentage(χ~2=4.284, P<0.05; χ~2=2.227, P<0.05) of boys, and the fat-free body weight(χ~2=3.287, P<0.05; χ~2=2.788, P<0.05) and body fat(χ~2=3.261, P<0.05; χ~2=2.135, P<0.05) of girls increased significantly in the intervention group. The fat-free body weight(χ~2=5.381, P<0.05; χ~2=3.278, P<0.05) and body fat(χ~2=5.987, P<0.05; χ~2=3.921, P<0.05) in both the intervention and the control groups increased significantly at T1 and T2 as compared with T0. Multivariate ANOVA result showed that, the fat-free body weight and body fat were significantly different between different time periods after age, height and body weight were controlled for boys but not girls. When body weights of different levels were included, the fat-free body weight(χ~2=6.234, P<0.05; χ~2=4.076, P<0.05) and body fat(χ~2=5.479, P<0.05; χ~2=2.315, P<0.05) increased significantly in low-, middle-and high-level subgroups of the intervention group at T1 and T2 as compared with the control group. The fat-free body weight(χ~2=5.784, P<0.05; χ~2=3.679, P<0.05) and body fat(χ~2=4.783, P<0.05; χ~2=2.784, P<0.05) in low-, middle-and high-level subgroups of both the intervention and the control groups increased significantly at T1 and T2 as compared to those at T0(P<0.05).Nutritional intervention(including milk and eggs) can promote the change in body composition in boys in Jinxiu Yao Autonomous County primary schools of Guangxi Zhuang Autonomous Region, but produces not too much benefit for girls.