Abstract: Objective To investigate the heart rate variability and target organ damage in patients with H-type hypertension complicated with acute cerebral infarction and their correlations. Methods From January, 2016 to January, 2017, 92 patients with hypertension complicated with cerebral infarction were prospectively collected in our hospital. According to the level of homocysteine (Hcy) on admission, all patients were assigned into observation group (Hcy ≥ 10 mmol, n=42) or control group (Hcy < 10 mmol/L, n=50). The heart rate variability and organs damage of the both groups were observed. Results When compared with the control group, the patients in the observation group got decreased level of SDNN, SDANN, SDNN-Index and PNN50 (%), P<0.05. There was no significant difference between the two group in rMSSD (P>0.05). The intima media thickness, arteriosclerosis index, coronary artery disease index, Cystatin C and 24 h systolic pressure variability in the observation group were significantly higher than those in the control group (P<0.05). Pearson linear correlation analysis showed that SDNN, SDANN and PNN50 (%) were negatively correlated with intimia-media thickness (IMT), cystatin C and 24 h systolic pressure variability (P<0.05); SDNN-Index was negatively related to cystatin C and 24 h systolic pressure variability (P<0.05). There was no significant correlation between rMSSD and IMT, arteriosclerosis index, coronary artery disease index, Cystatin C and 24 h systolic blood pressure variability (P>0.05). Conclusion Patients with H-type hypertension complicated with acute cerebral infarction get decreased heart rate variability and worse target organs functions, the decrease of heart rate variability may be related to the impairment of target organ function.