Orthodontic treatment hinges on tooth alignment, which significantly affects occlusal function, facial aesthetics, and patients' quality of life. Current deep learning approaches predominantly concentrate on predicting transformation matrices through imposing point-to-point geometric constraints for tooth alignment. Nevertheless, these matrices are likely associated with the anatomical structure of the human oral cavity and possess particular distribution characteristics that the deterministic point-to-point geometric constraints in prior work fail to capture. To address this, we introduce a new automatic tooth alignment method named TAlignDiff, which is supported by diffusion-based transformation learning. TAlignDiff comprises two main components: a primary point cloud-based regression network (PRN) and a diffusion-based transformation matrix denoising module (DTMD). Geometry-constrained losses supervise PRN learning for point cloud-level alignment. DTMD, as an auxiliary module, learns the latent distribution of transformation matrices from clinical data. We integrate point cloud-based transformation regression and diffusion-based transformation modeling into a unified framework, allowing bidirectional feedback between geometric constraints and diffusion refinement. Extensive ablation and comparative experiments demonstrate the effectiveness and superiority of our method, highlighting its potential in orthodontic treatment.