Objective: To investigate the differences in the intake of macronutrients between boarders and resident students in China, and to provide a scientific reference for relevant policies and preventive measures. Methods: The difference of macronutrients level between boarders and resident students were analyzed with the multilevel model (MLM) by using the data from Chinese Health and Nutrition Survey and the indicators of Chinese Dietary Reference Intakes (DRIs) 2013. Results: The daily intake of energy, carbohydrate, fat and protein were (1 597.59±557.15)kcal, (216.2±84.66)g, (57.88±31.96)g, (52.69±21.2)g respectively, with a rate of meeting DRIs of 17.32%, 84.17%, 50.30% for energy, carbohydrate and protein. There were significant differences in amount of energy, carbohydrate between boarders and resident students, but no significant difference in rate of meeting DRIs (15.09%, 87.28%, 17.54%, 83.86%, P>0.05 ). No difference in the amount of fat and protein intake between boarders and resident students, but the protein rate of meeting DRIs among resident students was significantly lower than that in boarders(34.91% vs 51.82%, χ2=4.45, P<0.01). Conclusion The results revealed an imbalanced intake of macronutrients among primary and secondary school students, which highlight the insufficiency in energy intake and the worse meeting rate of DRIs for protein among resident-student. The nutritional education targeting at boarder-students should be strengthened.