Background: Sibship size and structure have a significant association with overweight and obesity in children, but the relationship with thinness has not been fully studied and understood, especially in Asia. This study evaluated the associations among number of siblings, birth order, and childhood thinness and investigated the association of number of younger or older siblings with childhood thinness. Methods: In this study, we performed a population-based cross-sectional study among 84,075 3-to 12-year-old children in Shanghai using multistage stratified cluster random sampling. We defined grades 1, 2, and 3 thinness according to the body mass index cutoff points set by the International Obesity Task Force and used multinomial logistic regression models to estimate the odds ratio (OR) and 95% confidence interval (95% CI). Results: Compared with only children, for boys, children with two or more siblings were more likely to suffer from grade 2 (OR = 1.29, 95% CI 1.02, 1.64) and grade 3 thinness (OR = 1.60, 95% CI 1.07, 2.40); and the youngest child faced a higher risk of grade 2 (OR = 1.44, 95% CI 1.09, 1.90) and grade 3 thinness (OR = 1.53, 95% CI 1.01, 2.33). For girls, children with one sibling were more likely to suffer from grade 1 thinness (OR = 1.22, 95% CI 1.05, 1.42); the oldest child, middle child, and youngest child faced a higher risk of grade 1 (OR = 1.42, 95% CI 1.09, 1.84), grade 2 (OR = 1.26, 95% CI 1.03, 1.54), and grade 1 thinness (OR = 1.87, 95% CI 1.21, 2.88) respectively. There was no statistically significant relationship, however, between a larger number of younger or older siblings and childhood thinness. Conclusions: Regardless of sex, having either siblings or a higher birth order was positively associated with childhood thinness. The present study has suggested that future interventions to prevent childhood thinness should consider family background as an important factor, especially in multi-child-families.