In this paper, we extend our earlier polycube-based all-hexahedral mesh generation method to hexahedral-dominant mesh generation, and present the Hex-Dom software package. Given the boundary representation of a solid model, Hex-Dom creates a hex-dominant mesh by using a semi-automated polycube-based mesh generation method. The resulting hexahedral dominant mesh includes hexahedra, tetrahedra, and triangular prisms. By adding non-hexahedral elements, we are able to generate better quality hexahedral elements than in all-hexahedral meshes. We explain the underlying algorithms in four modules including segmentation, polycube construction, hex-dominant mesh generation and quality improvement, and use a rockerarm model to explain how to run the software. We also apply our software to a number of other complex models to test their robustness. The software package and all tested models are availabe in github (https://github.com/CMU-CBML/HexDom).