This paper is aimed to construct a 3D model of arterial vessels system of digital rat. Firstly, the special injection medium was perfused into the arterial blood vessels of Sprague-Dawley rat; the quality of perfusion through the digital radiography system was evaluated at the same time. Then we used the sectional anatomy imaging system and achieved the digital rat atlas of sectional anatomy (sectional anatomy images were captured at 100 microm intervals, with the resolution of 4,917 x 3,446 x 24 bit and in a total of 1,464 slices). Finally, the 3D model of arterial vessels system of digital rat was constructed by segmentation, and the visualization programs were developed on Visual C+ + and Visualization ToolKit (VTK). By use of this model, the 3D microstructure of arterial system of digital rat can be obtained accurately. Remarkably, it will benefit the study of the blood vessels system on laboratory rat.