Purpose of this study is to compare and analyze effect of exercise intensity in complex training for 8 weeks on leptin, growth hormone, IGF-1, and body composition in middle school with intellectual disability. Subjects of this study were 26 middle school students, 9 in high-intensity group, 9 in middle-intensity group, and 8 in low-intensity group. To compare the difference from different exercise intensity, pre-value before training has been set as covariate and different exercise intensity has been set as independent variable, with changes in leptin, growth hormone, IGF-1, and body composition. Analysis of covariance (ANOVA) has been performed for data analysis and effect size ƞ (eta) has been deduced. Result acquired from analyzed data is as following. First, when equal exercise has been imposed on middle school students with intellectual disability, in regard of exercise intensity, it was shown that leptin most decreased in middle-intensity, growth hormone most increased in middle-intensity, and IGF-1 increased in low-intensity. Second, in regard of body composition, low-intensity was most effective in increase of total body weight without fat. Decrease of body fat was most prominent in middle-intensity and increase of bone density, in low-intensity. Also, in further studies, study that differentiates subjects in gender and individual exercise performance is deemed mandatory.