The current method of SPECT/CT color medical image registration uses the location marker in vitro generally, such as SPECT/CT color medical image, but using the external-marker stent fixation with patient for examination is complicated relatively. A method of calculating registration parameters such as rotation angle and translation amount is proposed based on Quaternion color model. Firstly, the color medical image is represented as Quaternion vector matrix form. On the basis of this, a calculation method of Quaternion geometric moment is put forward about SPECT/CT color medical image. According to the distribution of Quaternion image quality, the relative rotation angle of two-mode image is obtained by using rotational inertia properties of Quaternion image. Then, the translation amount between two images is determined to realize registration by using Euclidean distance measure of mass center. The SPECT/CT color medical images are used in registration experiment. Good registration results are obtained, and this method is proved to be of effectiveness and feasibility.