Neurodevelopmental disorders (NDDs) are a group of diseases caused by abnormal development of the brain and nervous system, mainly including global developmental disabilities/intellectual disabilities, autism spectrum disorders, attention deficit hyperactivity disorder, and others; at present, certain progress has been made in the research on common NDDs, and some effective therapeutic approaches have been developed, but for rare NDDs such as fragile X syndrome, Rett syndrome, and Dravet syndrome, the elucidation of their pathogenesis and the development of therapeutic strategies still face major challenges due to insufficient clinical samples, the complexity of the brain structure, and the limitations of existing research models. In recent years, induced pluripotent stem cells (iPSCs) technology has achieved breakthrough progress, where the directed differentiation of patient-derived iPSCs into neurons, glial cells, and cerebral organoids, combined with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) gene-editing technology, provides a novel research model for exploring the pathogenic mechanisms and therapeutic strategies of rare NDDs, and this paper reviews the research advances and challenges of iPSCs technology in the study of rare NDDs.