The invention belongs to the field of medical image processing and application, and provides a retinal vessel three-dimensional reconstruction method based on a portable digital fundus camera. The method comprise steps that firstly, a portable digital fundus image is used, the camera is used for two fundus images by camera displacement, both images are require to contain retinal optic nerve disc structures, and a certain amount of offset is generated; and then, the retinal vessel is segmented, and the feature points are extracted, and based on retinal vessel anatomical hierarchy characteristicpoint matching and a three-dimensional vessel reconstruction model, the retinal vessel is subjected to three-dimensional reconstruction. The retinal vessel three-dimensional reconstruction method based on the portable digital fundus camera can provide new supplement to an existing fundus blood vessel observation and analysis based on two-dimension.