Oral rare diseases are a group of disorders characterized by distinct oral and craniofacial manifestations. These conditions are featured by low prevalence, high genetic and clinical heterogeneity, and great challenges in diagnosis and treatment. They can severely impair the development and physiological functions, posing substantial risks to both physical and mental health. In recent years, rapid advancements in genetics, molecular biology, and regenerative medicine have led to notable progress in the research of oral rare diseases. This review summarizes the current research landscape in this field, focusing on causative genes and mechanisms, diagnostic technologies, therapeutic approaches, clinical research, and digital innovations. It also discusses the existing challenges, aiming to promote further research and clinical translation in the field of oral rare diseases.