Digital rights management of the 3D contents is a crucial open issue in the 3D video industry. A novel robust fingerprinting algorithm is proposed for protecting the copyright of the 3D video. Unlike the existing algorithms extracting visual features separately from the 2D videos and the depth maps, in our algorithm a novel local stereo space is constructed according to the depth information of the pixels around the extracted local feature points in the 2D videos, and the 3D videos are processed in a holistic manner. In the proposed space, the 3D-transform-feature is extracted and aggregated into a feature matrix, and then the compact 3D video fingerprints are obtained from the eigenspace of the matrix. Our comprehensive experiments are conducted on a 3D video database, and the results have demonstrated the robustness and discrimination of the proposed algorithm. Moreover, our fingerprints cost less storage spaces than the existing approaches.