The objective was to explore the effect modification of zinc (Zn) intake levels on the relationship of tobacco smoke exposure and risk of metabolic syndrome (MetS) in children and adolescents. We used data from 2007-2018 National Health and Nutrition Examination Survey (N = 3701). MetS was considered as main endpoint. Weighted multivariable logistic regression models showed that high cotinine level (≥ 0.05 ng/mL) was associated with increased odds of MetS [odds ratio = 1.54, 95% confidence interval: 1.01, 2.36], and the association between Zn intake levels and MetS did not demonstrate statistical significance. Importantly, the multiplicative interaction term between low Zn intake (≤ 4.89 mg/1000 kcal) and high cotinine level was related to higher odds of MetS (p-value for interaction 0.018). For the group with low Zn intake, high cotinine level was associated with increased odds of MetS. However, there was no significant relationship between cotinine levels and MetS risk in the group with high Zn intake. The effect modification by Zn intake on the relationship of tobacco smoke exposure and risk of MetS is significant in individuals who had a sedentary time of ≥ 6 h, identified as non-Hispanic White, or resided in households with smokers. In short, low Zn intake may potentiate the association of tobacco smoke exposure and MetS risk in children and adolescents.