In this paper, we propose an efficient combinatorial optimization algorithm using the tree-structured Pazen Estimator (TPE). TPE is a widely used hyperparameter optimization (HPO) method, but it has been mainly focused on deep learning. In this paper, we generalize the categorical kernel and the numerical kernel and introduce a distance structure to the categorical kernel to apply TPE to fields where combinatorial optimization is important, such as chemistry and biology. In addition, we propose a modified method to reduce the time complexity of kernel computation to efficiently process a large combinatorial search space. Through experiments on synthetic problems, we verify that the proposed method finds better solutions with fewer evaluations than the existing TPE, and the algorithm is implemented in Optuna, an open-source HPO framework.