Objective To analyze the clinical data of the patients with leucine-rich glioma inactivated 1 （LGI-1） antibody-positive autoimmune encephalitis （AE） （LGI-1 AE） complicated with sleep structure abnormality and cognitive impairment， and to discuss the possible pathogenic mechanism. Methods A 68-year-old male patient was admitted to our hospital due to memory decline for 2 months and seizures for 1 month.After diagnosed with LGI-1 AE， the patient was treated with intravenous immunoglobulin combined with methylprednisolone sodium succinate， resulting in the improved symptoms. Excluding any pharmaceutical influences， the neuropsychological assessments， including sleep evaluations with polysomnography （PSG）， were performed during both the acute phase and the recovery phase. Results During the acute phase assessment， the patient exhibited severe cognitive impairments， scoring 22 on the Mini-Mental State Examination （MMSE） and 19 on the Montreal Cognitive Assessment （MoCA）.The PSG results showed that the total sleep time （265 min） was shortened， the sleep fragmentation throughout could be seen， the sleep efficiency was reduced， and N3 and rapid eye movement （REM） sleep stages were complete absent. In the recovery phase， the patient’s cognitive functions improved （MMSE score was 30， MoCA score was 26）， the total sleep time returned to normal with PSG， the sleep onset latency was 13.5 min， the sleep fragmentation notably improved， the sleep efficiency was increased to 84.3%，the N3 sleep lasted 26 min （5.1%）， and the REM sleep lasted 69 min （13.6%）. Conclusion The abnormality in sleep structure and cognitive impairment in the patients with LGI-1 AE are synchronous in onset and outcome， and may be one of the etiologies of cognitive dysfunction in these patients. The pathological origin of the sleep disorder may lie in the hypothalamus. Hypothalamic secretions and the Lhx6 pathway might become new targets for correcting the sleep structure while treating the cognitive impairment.