Objective To explore the characteristics and differences of brain morphology and cognitive function impairment in patients with bipolar affective disorder and schizophrenia on CT images. Methods 53 patients with bipolar disorder and 49 patients with schizophrenia who were treated in our hospital from January 2019 to December 2022 were selected, both groups were given brain CT to observe the brain morphology, the cognitive function of patients was evaluated by using the MATRICS Consensus Cognitive Test (MCCB), Wisconsin Card Sorting Test (WCST), digit span and digit sign test, and the severity of symptoms of schizophrenia was evaluated by using the Negative and Positive Symptom Scale (PANSS) Results There was no significant difference in the Hastelli value, the maximum width of the third ventricle, the body index of the lateral ventricle, the ventricular index and the brain atrophy score of the patients with bipolar affective disorder and schizophrenia (P＜0.05) The MCCB test scores of schizophrenia patients were significantly lower than those of bipolar disorder patients (P＜0.05) The number of WCST classification in schizophrenia was significantly lower than that in bipolar disorder (P＜ 0.05), while the number of errors and persistent errors was significantly higher in bipolar disorder (P＜0.05)The number span test inverted score and number coincidence test score of schizophrenia patients were significantly lower than those of bipolar disorder patients (P＜0.05). There was no significant difference in brain CT image parameters among patients with different PANSS scores in schizophrenia (P＞0.05) The total scores of speech memory, language ability, symbol coding, continuous operation, spatial breadth, number sequence and operation ability of patients with schizophrenia with PANSS score ≥ 60 were significantly lower than those with PANSS score＜60 (P＜0.05) The classification number of WCST test in patients with PANSS score ≥60 was significantly lower than that in patients with PANSS score ＜60 (P＜0.05), while the number of errors and persistent errors were significantly higher than those in patients with PANSS score ＜ 60 (P＜0.05) PANSS score ≥60 in patients with schizophrenia was significantly lower than PANSS score ＜ 60 in patients with number span test inverted score and number coincidence test score (P＜0.05) Conclusion There is no significant difference in brain morphology between patients with bipolar affective disorder and schizophrenia on CT images; Compare with bipolar affective disorder, the cognitive function of schizophrenic patients is more seriously damaged, which is related to the severity of symptoms