Does school environment shape students’ bodies? To answer this question, based on the data from the Survey of Primary and Middle School Students’ Learning Situations and Learning Environments (2020), we investigated, through an “individual-centered” research perspective, latent profile analysis and multilevel ordinal logistic regression, whether inter-school differences and time-use patterns in basic education have an impact on obesity among primary and junior secondary school students. This research found that, first, at the primary and middle school level, the school level and the school type have an effect on the obesity of students. The effect of school factors at the senior high school level was not significant. Second, there are significant time-use patterns in obesity levels and two characteristics with school level. At the primary and middle school levels, students with more quiet time for homework and video games are more likely to be obese. Third, the time-use patterns of obesity among primary and middle school students were variable with inter-school differences and was particularly evident at the middle school level. Students in public middle schools were more likely to show differences in the time-use patterns of obesity compared to students in private middle schools. Therefore, the structural characteristics of obesity in primary and middle school students should be fully considered in the formulation of school and student health policies. Policy interventions should be made through the time spent on homework, cell phones (games), sport and sleep, so as to effectively curb the occurrence of overweight and obesity.