The treatment of refractory schizophrenia has been a clinical challenge for most psychiatrists. The possible mechanism of the refractory schizophrenia included diagnostic errors, medical conditions and brain dysgensis. Here, we described a patient with childhood-onset schizophrenia who had severe psychiatric symptoms such as auditory hallucination and persecutory delusion and so on. We reexamined all his possible medical conditions and found the patient had an abnormal enlarged Cavus Septum Pellucidum (CSP) combined with Cavum Vergae (CV) (maximum length>30 mm). Some reports suggested that abnormal CSP(length>6 mm) has an significant association with schizophrenia. However, abnormally large CSP or CSP/CV and related prognosis were reported rarely. This case suggested that abnormally enlarged CSP or CSP/CV may lead to schizophrenia and worse prognosis.