The aim of the present study was to examine whether serum Zn concentrations were associated with metabolic risk factors in Chinese children and adolescents. This was a cross-sectional study including 3241 participants, aged 6 to 17 years, from Jiangsu, China. Metabolic risk factors included fasting glucose (FG), total cholesterol (TC), TAG, HDL-cholesterol, LDL-cholesterol, systolic blood pressure and diastolic blood pressure. Data were analysed using multi-variable linear regression and generalised additive models, which were adjusted for age, sex, high-sensitive C-reactive protein, estimated glomerular filtration rate, BMI and region of residence, to assess the associations of serum Zn concentrations with metabolic risk factors. We observed a negative association between serum Zn concentrations and FG (coefficient = −0·532; 95 % CI −0·569, −0·495; P < 0·001). Moreover, TC (coefficient = 0·175; 95 % CI 0·127, 0·222; P < 0·001), HDL-cholesterol (coefficient = 0·137; 95 % CI 0·082, 0·193; P < 0·001) and LDL-cholesterol (coefficient = 0·195; 95 % CI 0·128, 0·263; P < 0·001) were found to be positively associated with Zn levels. A generalised additive model showed that the negative association between serum Zn and FG was weak at lower serum Zn concentrations and was stronger with the increase in serum Zn concentrations. Additionally, a U-shaped association between serum Zn and TAG was observed. Serum Zn concentrations were associated with FG, TC, TAG, HDL-cholesterol and LDL-cholesterol levels in Chinese children and adolescents. Lower levels of serum Zn were more likely related to a poor metabolic status.