Objective To analyze the comorbidity of obstructive sleep apnea hypopnea syndrome (OSAHS) and stroke on neurological function, sleep, and cognition. Methods The cross-sectional study enrolled 396 patients from January 2015 through December 2017, including 98 with stroke only, 228 patients also complicated with OSAHS, presenting snoring and treated by the sleep center of the hospital, and 70 OSAHS patients. All groups had matched age, gender and education level, and all patients were tested by polysomnography(PSG) to obtain laboratory-based polysomnographic variables, including apnea hypopnea index(AHI), oxygen desaturation index and microarousal index, etc. The severity of stroke was assessed by National Institutes of Health Stroke Scale (NIHSS), motor function was determined with Fugl-Meyer assessment (FMA), cognitive function was evaluated based on mini-mental state examination (MMSE), and stroke-related disability was calculated with Barthel index(BI). Results The MMSE, body mass index (BMI) and status of underlying disease were significantly among groups (P<0.05). The patients with OSAHS had higher cognition and BMI (P<0.001), while higher prevalence of underlying diseases, such as hypertension, type 2 diabetes mellitus, coronary heart disease and atrial fibrillation was observed in patients with stroke patients and OSAHS (P<0.05). Comorbidity of OSAHS increased the risk of recurrence of stroke (P<0.001), however, did not affect the type, location and progression of stroke（P>0.05）. The AHI and MMSE were negatively correlated (r=-0.300, P<0.001), and the severity of OSAHS was positively correlated with the changes of FMA, NIHSS, MMSE, BI and sleep parameters in patients with the comorbidity(P<0.05). Conclusions The comorbidity of OSAHS and stoke has significantly compromised cognition, neurological impairment, motor function and daily activity of patient, and predispose higher risk of recurrent stroke.