This study aimed to explore the combined effects of serum vitamin-D level and tobacco exposure on the risk of overweight and obesity in children. This cross-sectional study analysed the data of 11 636 children aged 2–17 years from the National Health and Nutrition Examination Surveys database between 2007 and 2018. Univariable and multivariate weighted logistic regression models were used to analyse the associations of serum vitamin-D or cotinine levels with overweight and obesity in children as well as the combined effects of serum vitamin-D and cotinine on the risk of overweight and obesity in children. Subgroup analysis was performed in terms of gender, age, race and household smokers. OR with corresponding 95 % CI was presented. The elevated risk of overweight and obesity in children was found in those with serum vitamin-D < 20 ng/ml (OR = 1·44, 95 % CI: 1·29, 1·61). Also, the odds of overweight and obesity in children was 1·14 (OR = 1·14, 95 % CI: 1·01, 1·29) in children with cotinine ≥ 0·05 ng/ml. Relative to participants with serum vitamin-D ≥ 20 ng/ml and cotinine < 0·05 ng/ml, increased risk of overweight and obesity was identified in those with serum vitamin-D < 20 ng/ml and cotinine < 0·05 ng/ml (OR = 1·45, 95 % CI: 1·26, 1·68) and serum vitamin-D < 20 ng/ml and cotinine ≥ 0·05 ng/ml (OR = 1·62, 95 % CI: 1·38, 1·91). Serum vitamin-D and cotinine exposure had combined effects on the risk of overweight and obesity in children.