Background: Despite the environment being recognized as playing an important role in health, little is known about the influence of school and community factors on student health. This study aimed to identify the ecological factors influencing obesity among middle school students, including intrapersonal, interpersonal, school, and community factors. Methods: The study sample consisted of 2069 students from 50 middle schools, with individual-level data. School and community-level data were collected using a school nurse survey and official materials from the National and Civic Statistics. These data were merged and used for a series of multilevel logistic regression analyses. Results: There were significant variations in the students' overweight/obesity status, by ecological factors. Individual dietary habits, peer social support for physical activity, health education in the regular curriculum, the number of personal computer rooms per 100,000 individuals, and the area of public sports facilities per 100,000 individuals were significantly associated with student obesity. Conclusions: To be more effective, overweight/obesity prevention efforts for middle school students should focus not only on individual factors, but also on school and community factors.