The invention relates to an apparatus and method for identifying blood vessels in an angiography-assisted congenital heart disease operation. The apparatus comprises a CT image preprocessing module, a segmentation module, a three-dimensional reconstruction module, a two-dimensional planarization module, a contrast imaging module, a registration initialization module, a quantum updating module, an individual mutation module, a mutation post-processing module, an image registration module and a blood vessel identification result display module, wherein the CT image preprocessing module, the segmentation module, the three-dimensional reconstruction module and the two-dimensional planarization module are used before the operation, and the contrast imaging module, the registration initialization module, the quantum updating module, the individual mutation module, the mutation post-processing module, the image registration module and the blood vessel identification result display module are used in the operation. The method includes the following steps that: a preoperative image is segmented; three-dimensional visual reconstruction is performed on segmented CT images, so that segmented two-dimensional images of a preoperative heart and preoperative blood vessels are obtained; and the segmented two-dimensional images of the preoperative heart and preoperative blood vessels are registered with intra-operative contrast images, and results obtained after registration are displayed. With the apparatus and method of the invention adopted, the registration results have high precision and rich detail information, and therefore, the accurate positions of the blood vessels of a patient can be provided for a doctor in a congenital heart disease operation, and the difficulty of the operation can be reduced.