Computer-aided engineering (CAE) has emerged as an indispensable tool for facilitating engineering practices and driving industrial innovation. However, the insufficient quality and efficiency of discretizing complex computer-aided design (CAD) models significantly impede the advancement of CAE calculation accuracy and automation. The presence of “dirty” geometry leads to the fact that it is almost impossible to generate a traditional conforming mesh without geometry repair. In most instances, automating geometry repair proves to be even more challenging than meshing. To cope with intricate CAD model with “dirty” geometry, a novel binary tree surface subdivision method (BSSM) is proposed for automatically generated conforming and nonconforming meshes directly on CAD models. In contrast to the conventional conforming mesh, the nonconforming mesh allows for hanging nodes, thereby eliminating the limitations of the mesh conformance. This facilitates rapid transitions in mesh size for automatic mesh generation when dealing with “dirty” geometry. A series of numerical models employing BSSM are presented in this study. Results reveal that BSSM can automatically, efficiently and reliably generate high level quality mesh for arbitrary structures.