To enhance security and robustness of watermarking algorithms, this paper proposes a robust 3D model watermarking scheme based on non-uniform discrete Fourier transform (NDFT). In order to resist attacks such as non-uniform scale, rotation and translation, the affine invariant norm is applied to build partitions of vertices, which can be carried out by NDFT. The paper is also proved that the bit-embedding does not change the mass center of 3D model. The original model is not required in watermark detection. Simulation results show that the proposed scheme has high robustness against these attacks(including noise attack).