Obesity can cause various diseases and is a serious health concern. BMI, which is currently the popular measure for judging obesity, does not accurately classify obesity; it reflects the height and weight but ignores the characteristics of an individual’s body type. In order to overcome the limitations of classifying obesity using BMI, we considered 3-dimensional (3D) measurements of the human body. The scope of our study was limited to Korean subjects. In order to expand 3D body scan data clinically, 3D body scans, Dual-energy X-ray absorptiometry, and Bioelectrical Impedance Analysis data was collected pairwise for 160 Korean subjects. A machine learning-based obesity classification framework using 3D body scan data was designed, validated through Accuracy, Recall, Precision, and F1 score, and compared with BMI and BIA. In a test dataset of 40 people, BMI had the following values: Accuracy: 0.529, Recall: 0.472, Precision: 0.458, and F1 score: 0.462, while BIA had the following values: Accuracy: 0.752, Recall: 0.742, Precision: 0.751, and F1 score: 0.739. Our proposed model had the following values: Accuracy: 0.800, Recall: 0.767, Precision: 0.842, and F1 score: 0.792. Thus, our accuracy was higher than BMI as well as BIA. Our model can be used for obesity management through 3D body scans.