Deep watermarking has been successfully applied to real-value domain (e.g., CT, MRI, DWI) medical images for copyright protection; however, manifold-value domain images, such as diffusion tensor imaging (DTI), have received less academic attention. The non-Euclidean nature of DTI images hinders deep models from generating plausible DTI images because it is difficult to guarantee that each generated DTI image voxel lies on a 3 × 3 symmetric positive definite manifold. In this paper, we propose a robust watermarking scheme based on voxel space transformation for DTI images. First, a voxel space transformation is proposed, which effectively solves the problem of fiber orientation estimation in Riemann networks for DTI images and obtains the eigenvalues and eigenvectors of each voxel using singular value decomposition (SVD) to transform the DTI voxels from the 3 × 3 symmetric positive definite manifold space to Euclidean space. Second, SVD is combined with a deep neural network to extract the high-level features of each voxel eigenvalue in the DTI images and embedding watermarking messages, avoiding the false positive errors problem in traditional watermarking algorithms based on an SVD transform. Finally, using a deep neural network combining multiscale dilated convolution, dense residual connection and channel attention, the algorithm demonstrates high robustness against various intentional or unintentional attacks on DTI images while ensuring the good visual quality and diffusion characteristics of the DTI images embedded with watermarking messages. Experiments show that the watermarking message extraction accuracy reaches 97.8% for Crop (p = 0.7) attacks and 95.4% for Gaussian Blur (k = 7) attacks.