In order to solve the information security problem of medical images, on the basis of considering the special medical image, a novel watermarking algorithm for medical volume data is brought out. First of all, three-dimensional (3D) discrete wavelet transformation for the medical volume data is carried out. Secondly, the wavelet coefficients are transformed by 3D discrete Fourier transform, and the first lowfrequency coefficients (4*5*4) are selected. Then, the first low-frequency coefficients (4*5*4) are transformed by 3D discrete inverse Fourier transform to get the feature vector. At last, the algorithm uses the difference hashing algorithm to process the feature vector to generate zero-watermarking. The experimental results show the watermarking algorithm has good resistance to geometric attacks and has better security. So the watermarking algorithm is more practical in the field of medical research.