To investigate the association between milk intake at breakfast and nutritional status of students attending the Nutrition Improvement Program for Rural Compulsory Education Students (NIPRCES) in 2016, and to provide basic data for improving the nutritional status of the poor rural pupils. Using the multi-stage stratified random cluster sampling method, 22 315 students from grade three to nine from primary and junior high schools were randomly selected from the 50 key counties under the monitor programs, in 22 provinces of NNIPRCS. Questionnaire was used. Among all the students, with equal number of genders, morning fasting height and weight were measured by trained investigators. Status of nutrition was classified as malnutrition, normal, overweight/obesity, by age-specific height and BMI. Multivariate linear and logistic regression methods were used to analyze the relationship between milk consumption and the status of nutrition of the students. Only 31.4% of the students that were on the monitoring programs would drink milk at breakfast. Proportions of milk intake at breakfast were higher in students from the western regions, in lower grades and in girls (<0.05). The proportions of malnutrition and overweight/obesity were 11.0% and 10.0% respectively. After controlling factors as gender, age, ethnicity, region of residency and types of parental employment, students who drank milk at breakfast showed an average height of 0.4 cm taller than those who did not drink milk (=0.001). However, no significant relationships were noticed between milk intake at breakfast and weight, malnutrition or overweight/obesity. Milk intake at breakfast seemed associated with the height of the students under study, suggesting that this program can be promoted, especially in students from the poor rural areas.