Objective To investigate the effect of Hcy and NO/ET-1 on cognitive dysfunction in patients with obstructive sleep apnea hypopnea syndrome (OSAHS). Methods Totally 86 patients with OSAHS (OSAHS group) and 50 healthy controls (control group) were selected. The levels of serum Hcy and ratio of NO/ET-1 were determined. The Montreal cognitive assessment scale was used to evaluate the incidence of mild cognitive impairment. Correlation between the level of serum Hcy or NO/ET-1 and cognitive function was analyzed. Results The level of serum Hcy in patients with OSAHS was increased while NO/ET-1 was decreased when compared with those in normal control group (P?< 0.05). The AHI and sleep time in OSAHS group were higher while LSaO2 was lower significantly compared with those in normal group (P?< 0.05). MoCA score was negatively correlated with AHI, sleep time and serum Hcy (P?< 0.05). MoCA score was positively correlated with LSaO2 and NO/ET-1 (P?< 0.05). Cut-off point of ROC curve of serum Hcy and NO/ET-1 for prediction of cognitive impairment in COPD patients were 0.708 (95% CI: 0.599, 0.816) and 0.739 (95% CI: 0.618, 0.859), respectively. Conclusions Serum Hcy and NO/ET-1 may be independent prognostic factors for cognitive impairment in OSAHS patients.