Abstract: Microcirculation is the basic structure and function unit in the circulatory system, and it is prominent to keep the body's normal physiological function. Many diseases also start from the microcirculation. Therefore, the aim of this paper is to combine dorsal skin fold chamber with image processing and construct the three-dimension model of microcirculation to lay a foundation in in-vitro experiments and numerical analysis of the microcirculation. Stents with round chambers that can be loaded free were designed and fixed on the back of rats, then structure of the vessels in the chamber was observed by the stereomicroscope. In order to obtain vascular structures of microcirculation information such as boundaries and centerline, a series of image processing were employed. Meanwhile, the connections of bifurcation were determined according to the information of intersection in bifurcation. At the stage of the mesh, the improved transfinite interpolation algorithm was applied to build a three-dimensional finite element mesh model of the vascular network, and reconstruction of the three-dimensional model of any branch of the vascular network was achieved.