The invention relates to a dual-spectrum image registration system and method. The system comprises a dual-waveband image obtaining component, a calibration plate, a fluorescent lamp and an upper computer, wherein the dual-waveband image obtaining component comprises a first camera and a second camera, which are used for obtaining images of different waveband; the first camera is parallel to the second camera in the aspect of optic axis; both the first camera and the second camera are connected with the upper computer; at least four location holes are formed in the calibration late; the four location holes are connected to form a rectangular structure; and during the registration, the fluorescent lamp is located behind the location holes, the first camera and the second camera respectively acquire images of corresponding wavebands and send the images to the upper computer, and the upper computer calculates registration parameters according to the acquired images. Compared with the prior art, the registration method provided by the invention is simple, practical and correct and reliable in registration result.