This study aimed to examine the association between muscle mass and perception of body shape, desired body shape, physical strength, exercise habits, and eating behaviors. Height, weight, and body composition in 270 female university students were measured. The questionnaire on body shape perception, desired body shape, dieting experience, current, and past exercise habits, exercise preference, and eating behaviors were administered. The analysis of covariance with body fat mass as the covariate found that the skeletal muscle index (SMI) was different among each group on each of body perception or desired body shape (all, p < 0.001). In the post hoc test on body shape perception, the SMI in “obese” was significantly more than that in “slim” (p < 0.001) and “normal” (p < 0.001). In the desired body shape, the SMI in “become thin” was more than that in “maintain as current shape” (p < 0.001). Further, a significant difference was found among the categories of diet experience, with body fat mass as the covariate. In the post hoc test, the SMI in “yes” was more than that in “no” (p < 0.001). These results indicate that not only body fat mass but skeletal muscle mass drives young females’ desire for thinness even with exercise advantages.