In some fields of computational fluid dynamics, the nearest distance from a certain point in the flow field to the wall surface is usually required. In order to improve the precision as well as the efficiency of the computation result, the KD tree method was applied to the wall distance computation of unstructured mesh, and then the wall distances of several three dimensional configurations were computed. Results show that the method computing wall distances based on KD tree can achieve the capability of great robustness, high efficiency and precision, and is suitable for complex configuration. Besides, the method has good universality so that it can be applied to many other types of mesh.