Clear aligner, as a transparent and removable appliance, offers an alternative to conventional fixed appliance to patients with high demands for esthetics and comfort. Meanwhile, the rapid development of materials and techniques has made clear aligner more widely used in orthodontics. However, there are still several concerns and risks in clinical practice of clear aligners, which may result in unfavorable outcomes. Herein, we have discussed the clinical risks of clear aligner therapy, and provided some targeted strategies, in order to promote the clinical application of clear aligners.