Background and ObjectiveResearch on body composition phenotypes and bone health in adolescents is limited. Hence, this study aimed to analyze the relationship between different body composition phenotypes, bone mineral content, and bone metabolism markers in Chinese adolescents. MethodsIn this cross-sectional study, 1852 adolescents aged 12 to 18 years were selected from six schools in Yinchuan City between 2017 and 2020 using stratified cluster random sampling. The participant's body composition and bone mineral content (BMC) were measured using bioelectrical impedance analysis (BIA). Serum bone metabolic markers (OC, CTX, and Ca) were measured. Based on their FMI and LMI, individuals were categorized into four body composition phenotypes: low fat mass-low lean mass (LFMI-LLMI), low fat mass-high lean mass (LFMI-HLMI), high fat mass-high lean mass (HFMI-HLMI), high fat mass-low lean mass (HFMI-LLMI). ResultsThere was a statistically significant difference between the four different body composition phenotypes with BMC, CTX and Ca in boys (all P < 0.05), similar conclusions were found in girls, except the OC and CTX. After adjusting for age, gender, smoking, drinking, and others, compared with the LFMI-HLMI reference group, the two high FMI groups (HFMI-LLMI and HFMI-HLMI) had a greater negative correlation with BMC, while the low BMC risk of the HFMI-LLMI group was the highest (OR = 33.28; 95%CI: 11.12–99.63; P < 0.001). The correlation between BMC of different body composition phenotypes in boys was greater than that in girls. HFMI-HLMI is a risk phenotype negatively associated with Ca content (β = −0.12; 95%CI: −0.19 to −0.04; P < 0.05). Regardless of body composition level, BMC was always negatively correlated with fat mass (LLMI: β = −0.27; 95%CI: −0.32–0.21; HLMI: β = −0.52, 95%CI: −0.65–0.40) and positively correlated with lean mass (LFMI: β =0.24; 95%CI: 0.20–0.28; HFMI: β =0.23, 95%CI:0.13–0.33) (all P < 0.001). The fat mass showed different correlations with OC and CTX in girls and boys based on LLMI or HLMI (all P < 0.05). ConclusionHFMI-LLMI is a risk phenotype of low BMC in Chinese adolescents, and the relationship between fat mass and bone metabolism markers is affected by lean body mass and gender.