Objective: To understand the association between beverage and snack intake and insufficient serum 25 hydroxyvitamin D [25(OH)D] among primary and secondary school students, so as to provide a scientific basis for targeted intervention measures. Methods: From October to December 2021, a stratified random sampling method was used to select 2 477 primary and secondary school students aged 8 to 15 years old from 9 counties in Yunnan Province implemented the Nutrition Improvement Plan for Rural Compulsory Education Students. The intake of beverages and snacks was investigated using the Rural Student Nutrition Monitoring Questionnaire from Chinese Center for Disease Control and Prevention. The snack intake intensity was calculated and classified into no intake, extremely low, low, medium, and high intensity. Serum 25(OH)D levels were measured in the laboratory, and levels <20 ng/mL were defined as insufficient. Chi square tests, LASSO regression, random forest and binary Logistic regression were used to analyze the association between 20 types of beverages and snacks and serum 25(OH)D insufficiency. Results: Insufficient serum 25(OH)D was detected in 564 boys (45.9%) and 855 girls (68.5%), with a total of 1 419 cases (57.3%). Binary Logistic regression results showed that extremely low intake intensity of carbonated beverages ( OR =1.51), plant protein beverages ( OR =1.61), and milk tea beverages ( OR =1.39) increased the risk of insufficient serum 25(OH)D, while protective factors were fruits and vegetables ( OR =0.77) and pure milk and yogurt ( OR =0.74) (all P <0.05). Subgroup analysis showed that extremely low intake intensity of carbonated beverages, milk containing beverages, tea beverages, fruit and vegetable juices, and plant protein beverages increased the risk of insufficient serum 25(OH)D in girls ( OR =2.22, 1.72, 1.67, 1.74, 1.92), and high intake intensity increased the risk of insufficient serum 25(OH)D in boys ( OR =1.73, 1.48, 1.52, 1.49, 1.97) (all P <0.05). Extremely low intake intensity of carbonated beverages, plant protein beverages, and milk tea beverages in junior high school students ( OR =1.92, 2.54, 1.68) and low intake intensity in primary school students ( OR =1.40, 1.33, 1.45) increased the risk of insufficient serum 25(OH)D (all P <0.05). Conclusions Frequent intake of beverages and highly processed snacks increases the risk of insufficient serum 25(OH)D in primary and secondary school students, while natural foods such as fruits, vegetables, pure milk and yogurt can reduce the risk. Girls and junior high school students are more susceptible to these effects.