While tooth alignment is crucial for digital dentistry, especially in orthodontic treatment, existing computer-aided methods mainly focus on the 3D dental crown but overlook the entire teeth, which is essential for applications in orthodontics. Besides, clinical orthodontic rules are not fully considered in these methods, i.e., there should be no collisions and gaps between teeth, the upper jaw and lower jaw should have correct occlusion relationships, the teeth should comply with a reasonable dental arch curve, etc. To generate optimal tooth alignment results, we propose a rule-based optimization method for solving the tooth alignment problem that takes into consideration the clinical rules functionally and aesthetically. We optimize rule-driven objective functions by adjusting the 6-DoF transformations of each tooth. Besides, our optimization formulation supports customization for different clinical scenarios by specifying the various energy terms. Extensive experiments, ablation studies, and user studies have been conducted to validate the effectiveness of our method. Quantitative and qualitative comparisons demonstrate that our method generates better tooth alignments than previous methods.