Autoinflammatory diseases (AIDs) are characterized by abnormal activation of the innate immune system. Schnitzler syndrome, SAPHO (synovitis, acne, pustulosis, hyperostosis, and osteitis) syndrome, Yao syndrome, and PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome are rare polygenic AIDs. Although these diseases differ in etiology and pathogenesis, they all present with complex nonspecific clinical symptoms, such as periodic fever, inflammatory lesions of bones or skin, which makes diagnosis challenging and often leads to delayed treatment or even misdiagnosis. In recent years, rapid advances in molecular biology and genomics have gradually elucidated the pathogenesis of these rare diseases, offering new insights for optimizing diagnosis and treatment. This review summarizes the progress in the pathogenesis, clinical manifestations, diagnosis, and treatment of these rare polygenic AIDs, aiming to provide references for further refining management strategies for such diseases.