ObjectiveThe aim of this study was to identify the differential metabolic characteristics of children with overweight and obesity and understand their potential mechanism in different age stratifications.MethodsFour hundred seventy‐three children were recruited and divided into two age stratifications: >4 years (older children) and ≤4 years (younger children), and overweight and obesity were defined according to their BMI percentile. A one dimensional proton nuclear magnetic resonance (1H‐NMR)–based metabolomics strategy combined with pattern recognition methods was used to identify the metabolic characteristics of childhood overweight and obesity.ResultsFour and sixteen potential biomarkers related to overweight and two and twenty potential biomarkers related to obesity were identified from younger and older children, respectively. Fluctuations in phenylalanine, tyrosine, glutamine, leucine, histidine, and ascorbate co‐occurred in children with obesity at two age stratifications. The disturbances in biosynthesis and metabolism of amino acids, lipid metabolism, and galactose metabolism disturbance were mainly involved in children with overweight and obesity.ConclusionsThe metabolic disturbances show a significant progression from overweight to obesity in children, and different metabolic characteristics were demonstrated in age stratifications. The changes in the levels of phenylalanine, tyrosine, glutamine, leucine, histidine, and ascorbate were tracked with the persistence of childhood obesity. These findings will promote the mechanistic understanding of childhood overweight and obesity.