Accurate and high-quality tooth mesh generation from cone-beam computerized tomography (CBCT) is an essential computer-aided technology for digital dentistry. However, existing segmentation-based methods require complicated post-processing and significant manual correction to generate regular tooth meshes. In this paper, we propose a method of continuous bijection supervised pyramid diffeomorphic deformation (PDD) for learning tooth meshes, which could be used to directly generate high-quality tooth meshes from CBCT Images. Overall, we adopt a classic two-stage framework. In the first stage, we devise an enhanced detector to accurately locate and crop every tooth. In the second stage, a PDD network is designed to deform a sphere mesh from low resolution to high one according to pyramid flows based on diffeomorphic mesh deformations, so that the generated mesh approximates the ground truth infinitely and efficiently. To achieve that, a novel continuous bijection distance loss on the diffeomorphic sphere is also designed to supervise the deformation learning, which overcomes the shortcoming of loss based on nearest-neighbour mapping and improves the fitting precision. Experiments show that our method outperforms the state-of-the-art methods in terms of both different evaluation metrics and the geometry quality of reconstructed tooth surfaces.