Abstract: 3D X-ray Microscope is becoming a widely used imaging tool in many research and industrial fields such as biology, geology, material science, etc, due to its capability of achieving sub-micron spatial resolution and showing internal structures non-destructively. This paper introduces a newly developed X-ray Microscope (nano Voxel-2000) by Tianjin Sanying precision Instruments Ltd.. The system configuration and imaging technologies of the instrument are presented and discussed. One of the most important index for microscopes is resolution. nano Voxel-2000 is of a spatial resolution up to 500 nm. It can scan samples with different scales and fields of view via a multiple lens-coupled CCD detector system, and realize image reconstruction at different resolution scales. In addition, typical applications of the 3D X-ray Microscope in material science and geology are explored, and quantitative analysis on image data such as the morphology of material structures, interior structure information, etc. is presented. It is expected that this article can play a role in attracting more colleagues to carry out research with 3D X-ray Microscopy.