In a traditional topology optimization method, material properties are usually distributed by finite element density and visualized by a gray level image. The distribution method based on element density is adequate for a great mass of 2-D topology optimization problems. However, when it is used for 3-D topology optimization, it is always difficult to obtain a smooth model representation, and easily appears a virtualconnect phenomenon especially in a low-density domain. The 3-D structural topology optimization method has been developed using the node density instead of the element density that is based on SIMP (solid isotropic microstructure with penalization) algorithm. A computer code based on Matlab was written to validate the proposed method. When it was compared to the element density as design variable, this method could get a more uniform density distribution. To show the usefulness of this method, several typical examples of structure topology optimization are presented.