Skin is the largest organ in the human body and works as the natural barrier against the external environment. Furthermore, topical and transdermal drug delivery has been emerged as the new effective and safer administration. A variety of in vitro, in vivo, and ex vivo assays have been adopted to evaluate the retention of the drug in the skin layers and skin permeability, in which the ex vivo excised human skin has been considered as the gold standard to assess the skin penetration despite its potential of ethical issues. In this study, the novel machine learning-based hierarchical support vector regression (HSVR) was adopted to generate a nonlinear quantitative structure-activity relationship (QSAR) model, which can predict the Kp values based on the ex vivo human skin permeability data. The HSVR model showed consistent performance with the experimental data and among the training set, test set, outlier set, and mock test, which was designated to mimic the real challenges. In addition, the HSVR exhibited better prediction performance than the classical partial least squares (PLS). Thus, it can be concluded that the novel HSVR model can be utilized to facilitate the assessment of skin permeability of the novel compounds in drug discovery.