Background Physical activity has many health benefits for children and adolescents. However, the prevalence of physical inactivity in school-aged children and adolescents remains high in China. Many factors impact student’s moderate- and vigorous- physical activity (MVPA). This study investigated the factors associated with student's MVPA level, and the determinants of the change of student’s MVPA behavior.Methods This is a longitudinal study with a 12-month follow-up. The study samples came from 2016 and 2017 Physical Activity and Fitness in China—The Youth Study, 1597 students (aged 9-18 years) from 31 primary, junior high, and high schools, in Ningxia province, were included. Factors about the individual and external environment were measured by questionnaire at baseline and after 12 months. Multiple logistic regression was analyzed to examine the factors that impact student’s MVPA level and the determinants of the change of student’s MVPA behavior.Results There is no difference in students MVPA level between 2016 and 2017. Boys were more physically active than girls at baseline(RR 1.55, 95%CI 1.10, 2.20), as well as children than adolescents but not significant(RR 1.33, 95%CI 0.93, 1.90). Neighborhood factors associated students MVPA level significant, but all of these factors were removed from the longitudinal model(neighborhood sport event, organization, facility, et al). Individual and school factors were important for students MVPA maintaining and positively development(i.e. gender, attitude, school PE class and PA time, et al).Conclusions In conclusion, both neighborhood and school factors affect students MVPA behavior, but school play a more meaningful role in maintaining and promoting students MVPA level. In addition, the internal motivation may be more important than external environment for students MVPA level. Our research provide some evidences for future intervention program for promoting MVPA behavior, but more large samples and objective-assessed researches should be conduct to explore the determinants of MVPA.