The invention provides a method and a system for registering three-dimensional medical images on the basis of weighted fuzzy mutual information, and relates to the technical field of image-guided radiotherapy and medical image analysis. The method mainly includes steps of 1, guiding the medical images; 2, displaying the medical images; 3, processing the medical images; and 4, registering the medical images. In the step of guiding the medical images, single-mode image registration and multi-mode image registration are supported; in the step of displaying the medical images, cross section, coronal plane and sagittal plane images of the medical images to be registered are colored differently by a pseudo-color technology; in the step of processing the medical images, grayscales of the medical images are classified and compressed on the basis of a concept of fuzzy entropy, and mutual information calculation is reduced; and in the step of registering the medical images, normalized mutual information measures are modified on the basis of the fuzzy entropy, and the robustness of medical image registration is improved. The method and the system have the advantages that the measure method on the basis of the mutual information is adopted, the method and the system are applicable to single-mode image registration, and a good effect can also be realized for multi-mode image registration.