Exercise is important for body composition promotion. Although many studies have indicated that physical competence promotes exercise participation, there are relatively few studies examining the relationships among these factors. The purpose of the present study was to model the relationships among body composition, exercise habits and physical competence by using structural equation modeling. The subjects were 223 Japanese male and female high school students. Height, lean bone mass and bone area ratio were measured. Exercise habits and physical competence scale including three subscales (perceived physical competence, feeling of control and peer and teacher acceptance) were assessed by self-administered questionnaires. Data were analyzed using structural equation modeling. The model showed acceptable fit indices (GFI = .905, AGFI = .863 CFI = .954, RMSEA = .069). The path from peer and teacher acceptance to exercise habit was significant (β = 0.51, p < .001). Moreover, the path from exercise habits and from perceived physical competence to body composition was significant (respectively β = 0.53; p < .001, β = 0.47, p < .001). We could model the relationships among body composition, exercise habits and physical competence. These results indicate that not only exercise habits but also physical competence promoting exercise participation influence on body composition promotion.