It is most important to reach the maximum bone density in the childhood period to prevent developing osteoporosis; it is widely known that increased body weight has a positive correlation with bone density and that even though both the fat mass and lean mass have a significant impact on bone density, the latter mass has more importance for adults. Therefore, the study analyzed to identify the relationship between bone density and both fat mass and lean mass of Korean adolescents. Subjects were chosen among 21,303 people from the Korea National Health and Nutrition Examination Survey (KNHNES) between 2008 and 2011 that took a bone density checkup; as a result, 1454 teenagers aged between 12 and 18 were selected. Data analysis was performed in SAS ver. 9.4 (SAS Institute Inc., Cary, NC, USA) following the KNHNES and the weighted complex sample analysis was conducted; body fat mass and lean mass were divided into quintile groups, and to figure out the differences in bone density that were analyzed in six models adjusted by body weight (kg) and walking (yes/no), muscle strengthening exercises (yes/no), nutrition (intake of ca (g), and serum vitamin D (ng/mL)). Then, the generalized linear model (GLM) and trend test were conducted for each gender with a significance level of 0.05. The bone density differences of fat mass and lean mass were analyzed. The result of Model 6 considering all correction variables is as follows; in the case of male adolescents, the total femur and lumbar spine showed a significant difference (F = 13.120, p < 0.001; F = 12.900, p < 0.001) for fat mass, and the trend test showed that the figures significantly decreased (β = −0.030, p < 0.001; −0.035, p < 0.001). Meanwhile, for lean mass, the total femur and lumbar spine had a significant difference (F = 16.740, p < 0.001; F = 20.590, p < 0.001) too, but the trend test showed a significant increase (β = 0.054, p < 0.001; 0.057, p < 0.001). In the case of female adolescents, the lumbar spine (F = 3.600, p < 0.05) for lean mass showed a significant difference, and it also significantly rose in the trend test too (β = 0.020, p < 0.01). To sum up the results, for male adolescents, the bone density differences for fat mass (FM) and lean mass (LM) all had significant differences, but for female adolescents, only the lumbar spine for LM showed such a result. Meanwhile, both genders showed that LM had a more positive impact on bone density than FM.