Measurements of body composition by dual-energy X-ray absorptiometry (DXA) have evident value in evaluating skeletal and muscular status in growing children and adolescents. This study aimed to generate age-related trends for body composition in Chinese children and adolescents, and to establish gender-specific reference percentile curves for the assessment of muscle-bone status. A total of 1541 Chinese children and adolescents aged from 5 to 19 years were recruited from southern China. Bone mineral content (BMC), lean mass (LM) and fat mass (FM) were measured for total body and total body less head (TBLH). After 14 years, total body LM was significantly higher in boys than girls (p < 0.001). However, total body FM was significantly higher in girls than boys in age groups 13-19 years (p < 0.01). Both LM and FM were consistent independent predictors of total body and subcranial bone mass in both sexes, even after adjustment for the well-known predictors of BMC. The results of multiple linear regression identified LM as the stronger predictor of total body and subcranial skeleton BMC while the fat mass contributed less. For all the subjects, significant positive correlations were observed between total body LM, height, total body BMC and subcranial BMC (p < 0.01). Subcranial BMC had a better correlation with LM than total body BMC. We have also presented gender-specific percentile curves for LM-for-height and BMC-for-LM which could be used to evaluate and follow various pediatric disorders with skeletal manifestations in this population.