Previous research on the association between cesarean section (CS) and childhood obesity has yielded inconsistent findings. This study assessed the secular trend of CS and explored the relationship between CS and the risks of overweight and obesity in Chinese children and adolescents. Data came from a national multicenter school-based study conducted in seven provinces of China in 2013. Covariate data including weight, height and delivery mode were extracted. Poisson regression was applied to determine the risk ratios (RRs) and 95% confidence intervals (CIs) for the risks of overweight and obesity associated with the delivery mode. A total of 18,780 (41.2%) subjects were born by CS between 1997 and 2006. The rate of CS increased from 27.2% in 1997 to 54.1% in 2006. After adjusting for major confounders, the RRs (95% CI) of overweight and obesity among subjects born by CS were 1.21 (1.15 to 1.27) and 1.51 (1.42 to 1.61), respectively. Similar results were observed in different subgroups stratified by sex, age, and region. In summary, the CS rate increased sharply in China between 1997 and 2006. CS was associated with increased risks of overweight and obesity in offspring after accounting for major confounding factors.