Objective To investigate the correlation of plasma homocysteine (Hcy) level with carotid intima-media thickness (IMT) and carotid atherosclerosis in Uygur and Han patients with hypertension living in Xinjiang Region. Methods A total of 420 essential hypertension patients admitted to Department of Geriatrics in our hospital from 2011 to 2015 were enrolled in this study. There were 214 subjects of Han nationality, at an age of (63.36±14.82) years, and 206 subjects of Uygur nationality, at an age of (64.16±15.79) years. Another 405 healthy individuals who taking physical examination in that period served as normal controls, and they were 203 of Han nationality (60.45±14.11 years old) and 202 of Uygur nationality (61.23±12.71 years old). Enzyme-linked immunosorbent assay was applied to determine the plasma level of Hcy, and color Doppler ultrasonography was applied to measure the carotid IMT. Results Compared with the normal controls, the hypertension group had higher body mass index (BMI), systolic blood pressure (SDP), diastolic blood pressure (DBP), and plasma Hcy level, but lower folic acid (FA), thicker carotid IMT and higher incidence of carotid plaques (P<0.05). There were no obvious differences between the Han and Uygur hypertensive patients in age, sex, uric acid (UA), triglycerides (TG), total cholesterol (TC), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), FA, carotid IMT and incidence of atherosclerotic plaques (P>0.05). Plasma Hcy level was positively correlated with age, TC, LDL-C and SBP, but negatively with FA. Carotid IMT was positively correlated with age, TC, LDL-C, SBP and Hcy level, but negatively with FA. Conclusion Age, TC, LDL-C and hyperhomocysteine are risk factors of carotid atherosclerosis for Uygur and Han hypertensive patients living in Xinjiang.