The present invention discloses a registration method and system for a non-rigid multi-modal medical image. The registration method comprises: obtaining local descriptors of a reference image according to Zernike moments of order 0 and repetition 0 and Zernike moments of order 1 and repetition 1 of the reference image; obtaining local descriptors of a floating image according to Zernike moments of order 0 and repetition 0 and Zernike moments of order 1 and repetition 1 of the floating image; and finally obtaining a registration image according to the local descriptors of the reference image and the floating image. In the present, by using self-similarity of the multi-modal medical image and adopting the Zernike moment based local descriptor, the non-rigid multi-modal medical image registration is thus converted into the non-rigid mono-modal medical image registration, thereby greatly improving its accuracy and robustness.