This study's main objective was to investigate the difference between snacking behaviors and dietary nutrient intake in boarding system students. A cross-sectional study was conducted at Beijing's closed and semi closed boarding management school. The snack consumption questionnaire collected snack consumption behaviors; three-day recall periods for food consumption data were collected through the canteen weighing method and 24-h dietary recall of students' intakes. For closed and semi closed boarding management schools, the percentage of never having snacking behaviors was 12.95% and 2.69% on weekdays and 2.16% and 4.19% on weekends. A higher proportion of respondents chose unhealthy snacks in closed boarding management schools. The main problems in closed boarding management schools were the excessively low percentage of energy from carbohydrates and the excessively high percentage of energy from fat. Both deficiency and excess energy supply ratios of protein, carbohydrate, and fat were present in semi-closed boarding management schools. There was a high risk of calcium, iron, zinc, magnesium, and selenium deficiency for most students in both management schools. The closed-school girls had the highest risk of suffering from iron deficiency. Vitamin A, vitamin B1, vitamin B2, vitamin C, and vitamin E deficiencies were severe in both schools, especially vitamin C, vitamin A, and vitamin B2 deficiencies in semi-closed boarding management schoolboys. Effective nutritional interventions should be taken to improve the nutritional status of both boarding management and school students.