Automatic tooth alignment target prediction is vital in shortening the planning time of orthodontic treatments and aligner designs. Generally, the quality of alignment targets greatly depends on the experience and ability of dentists and has enormous subjective factors. Therefore, many knowledge-driven alignment prediction methods have been proposed to help inexperienced dentists. Unfortunately, existing methods tend to directly regress tooth motion, which lacks clinical interpretability. Tooth anatomical landmarks play a critical role in orthodontics because they are effective in aiding the assessment of whether teeth are in close arrangement and normal occlusion. Thus, we consider anatomical landmark constraints to improve tooth alignment results. In this article, we present a novel tooth alignment neural network for alignment target predictions based on tooth landmark constraints and a hierarchical graph structure. We detect the landmarks of each tooth first and then construct a hierarchical graph of jaw-tooth-landmark to characterize the relationship between teeth and landmarks. Then, we define the landmark constraints to guide the network to learn the normal occlusion and predict the rigid transformation of each tooth during alignment. Our method achieves better results with the architecture built for tooth data and landmark constraints and has better explainability than previous methods with regard to clinical tooth alignments.