Objective To study the differences of obstructive sleep apnea hypopnea syndrome (OSAHS)-related indexes between Uyghur and Han, and to provide evidence for the development of individualized treatment measures for different ethnic groups. Methods 224 Han OSAHS patients were collected from Guangdong Provincial Hospital of Chinese Medicine, and 178 Uygur OSAHS patients were collected from The First People’s Hospital of Kashi between January 2018 and December 2019. The collected data information included age, sex, nationality, body mass index (BMI), apnea hypopnea index (AHI), lowest oxygen saturation (LSaO2), OSAHS stage, mean corpuscular hemoglobin concentration (MCHC), triglyceride (TG), total cholesterol (TC), high density lipoprotein (HDL), low density lipoprotein (LDL), fasting blood glucose (FBG), and glycosylated hemoglobin (HbAlc). After using propensity matching scores to reduce confounding factors, differences in above indicators between different nationalities were compared. Results The mean values of MCHC, TC and HDL in Uygur OSAHS patients were lower than those in Han patients at the same stage, and the mean values of LSaO2 and LDL in mild and severe Uygur OSAHS patients were lower than those in Han patients at the same stage, with statistically significant differences (all P<0.05). There were no significant differences in AHI, TG, FBG or HbAlc between Uygur and Han patients with OSAHS. Conclusion There are significant differences in LSaO2, LDL, MCHC, TC and HDL between Uygur and Han Chinese patients with OSAHS.