In the paper, robust multiple watermarks of medical volume data using 3D-DWT and 3D-DFT is proposed. The part of sign sequence of 3D-DWT and 3D-DFT coefficients are used as feature vector, which is utilized to enhance the robustness against Gaussian noise, JPEG compression, Median filter and Cropping attacks. Moreover, the content of medical volume data remains unchanged with our proposed algorithm which is one kind of the zero-watermarking technology. We describe how to obtain the feature vector of medical volume data and embed and extract the multiple watermarks. Simulation results demonstrate the proposed algorithm's robustness.