Objective: To investigate milk consumption and associated factors in the national pilot counties of Nutrition Improvement Programme for Rural Compulsory Education Students (NIPRCES) in 2016, and to provide basic data for milk consumption improvement. Methods: Two primary and middle schools in each county were selected randomly from 50 key monitoring counties in 22 provinces in NIPRCES by three food supply modes (school-based, company-based, and others). Then 1 or 2 classes in each grade were selected randomly from grade 3 or above and junior schools. A total of 25 948 students were collected, milk consumption and related factors were investigated through student questionnaires. Results: Among the students surveyed, the proportion of students drank 1 to 3 packs of milk every week was highest (45.4%), only 29.1% students drank 4 or more packets of milk per week. The proportion of children in grades 3 and 4 who drank 4 or more packets of milk per week (35.7%) was higher than that of children in grades 5 and 6 (31.8%) and junior school (22.5%)(P<0.01). The proportion of boys who drank 4 or more packs of milk per week (30.7%) was higher than girls (27.5%) (P<0.01). Multivariate Logistic regression analysis showed that boys, primary school students in grades 3 to 6, non-resident students, students with both parents or one parent at home, students who had more meals per day, students who had breakfast every day, students who took snacks or drank beverages once or more per day, students who drank 4 or more cups of boiled water were more likely to drink 4 or more packs of milk each week. Conclusion Students in poor rural areas in China lack access to milk. It is recommended that targeted measures should be taken to encourage and promote rural students to drink enough milk.