Objective To establish a three-dimensional (3D) visualization model for the vessel system of rabbit eyes using X-ray phase contrast imaging（XPCI）technique, and observe the morphological characteristics of iris vessels of the rabbit eyes. Methods Angiography on vessels of the New Zealand rabbit eyes was conducted using Barium sulfate as the contrast medium. The projected images of in vitro rabbit eye samples with high precision were obtained by XPCI technique, and then converted to tomography images by filter back projection. The 3D reconstruction of the rabbit eyes was completed by commercial visualization software Amira 5.2.2. Results The main blood vessels of the rabbit eyes were clear and coherent in the projection images, and the distribution and trend of some small vessels could be observed, with the smallest distinguishable blood vessel diameter being about 10 μm. The 3D model for vessel network of the rabbit eyes was built after 3D reconstruction of CT scan images. The major arterial circle of the iris could be observed at level 4 branch structure of vessels in the fundus, and the minimum diameter of vessels that could be identified was 40 μm. Conclusions The vessels of the rabbit eyes can be clearly observed and 3D visualization of vessel network can be constructed by using XPCI technique, which would provide basis for the analysis on hemodynamics of blood vessels in the eye and reference for the clinical study of glaucoma.