We present a novel learning-based method for predicting tooth movements in orthodontic treatment path planning (orthodontic staging). Recognizing the multi-solution nature of orthodontic staging, our approach involves generating the staging sequence progressively with a dedicated Transformer model. This model predicts teeth movements within a predefined number of steps (e.g., 10 or 20), targeting alignment in problematic dentition. The Transformer refines its predictions iteratively, building on previous outcomes until reaching a state that aligns with the target within an acceptable distance. This mirrors real-life scenarios where orthodontists dynamically adjust staging plans based on treatment outcomes. Our Transformer model is tailored to incorporate spatial and temporal attentions, addressing inter-tooth and inter-step interactions, respectively. These attentions are further refined with relative positional encoding. Recognizing the significant influence of tooth shape on the alignment process, we propose integrating a tooth-wise shape encoder to extract morphological features from the 3D teeth point cloud. These features are then fused into the Transformer, facilitating the capture of inter-tooth dynamics during staging, in collaboration with spatial attention. We validate the proposed method on a large-scale dataset that contains 10K real-life orthodontic cases. The results show that our method outperforms the state-of-the-art, and orthodontists favor its predictions.