Objective This study aimed to describe the prevalence rates of abnormal metabolic phenotypes among urban Chinese children and to explore the impact of body composition as measured by dual-energy x-ray absorptiometry (DXA) on metabolic disorders. Methods A total of 7,926 children aged 6 to 17 years from seven cities across China were involved. Metabolically unhealthy was defined as having >= 2 risk factors (elevated blood pressure, high triglyceride levels, low levels of high-density lipoprotein cholesterol, and impaired fasting glucose [IFG]). Abnormal metabolic phenotypes were defined as metabolically unhealthy with normal weight (MUNW) and metabolically healthy with overweight or obesity (MHO). Results Overall prevalence rates of MUNW and MHO were 10.6% and 15.3%, respectively. The prevalence of MUNW increased with age in boys, whereas the prevalence in girls was statistically higher in 11- to 15-year-olds than in other age groups. The prevalence of MHO decreased with age in both genders. Among children with normal weight, the levels of body composition indices were positively correlated with metabolically unhealthy phenotype. Fat-free mass had a protective effect on IFG in children with normal weight. Among children with overweight or obesity, body composition was related to elevated blood pressure and dyslipidemia but not to IFG. Conclusions The prevalence rates of abnormal metabolic phenotypes differed between genders and ages. Body composition could partly explain the different metabolic phenotypes at the same BMI status among children.