Background: Bone mineral acquisition during adolescence is crucial for maximizing peak bone mass. Fat mass (FM) and bone mass are closely related. This study investigated the association of FM distribution with bone mass in Chinese male adolescents. Method: A total of 693 male adolescents aged 10–18 years were recruited from a secondary school in Jiangmen, China. Their bone mass and body composition were measured by quantitative ultrasound and bioelectrical impedance analysis, respectively. The associations of the measures of fat distribution with bone parameters, i.e., broadband ultrasound attenuation, speed of sound (SOS), and stiffness index (SI), were analyzed using multiple linear regression. Age, height, body mass index, stage of puberty, physical activity, sedentary behavior, dietary energy intake, and dietary calcium and vitamin D intake were adjusted in the model. Further subgroup analyses of prepubertal and pubertal participants were conducted. Results: The measures of fat distribution showed negative associations with SOS and SI in total subjects (p < 0.010). In prepubertal boys, the measures of fat distribution were only associated with SOS (β = −0.377 to −0.393, p < 0.050). In pubertal boys, the measures of fat distribution had associations with all bone parameters (β = −0.205 to −0.584, p < 0.050). The strongest association was between trunk FM and SOS (β = −0.584, p < 0.001). Conclusion: This study supported that the measures of fat distribution were negatively associated with bone parameters in Chinese male adolescents. Trunk FM had the strongest association with bone parameter. These associations appear to be stronger in pubertal boys than in prepubertal boys.