Abstract: Objective To investigate the relationship between a blood pressure variability (BPV)-based scoring system (BPVSS) and the target organ damage in patients with hypertension. Methods We selected 95 consecutive inpatients with essential hypertension admitted between January and June, 2015 in the Department of Cardiology of Guangzhou General Hospital of Guangzhou Military Command. The BPV indices were analyzed for their correlation with the parameters of target organ damage (IVSd, LVPWd, baPWV_L/R, and IMT_L/R). The patients with a BPVSS of 3.9 or higher (control, 43 cases) and those with a lower BPVSS (observation group, 52 cases) were compared for differences in IVSd, LVPWd, baPWV_L/R, IMT_L/R and the proportion of carotid plaques. Results Similar with the traditional BPV indices, BPVSS was negatively correlated with IMT_L/R (r=-0.278/-0.324, P<0.05). BPVSS was also negatively correlated with IVSd (r=-0.241), LVPWd (r=-0.223), and baPWV_L/ R (r=-0.468/-0.373) (P<0.05). IVSd, LVPWd, baPWV_L/R and IMT_L/R were all significantly higher in the observation group than in the control group (t=2.307, 2.516, 3.250/2.790, and 2.372/3.425, respectively; P<0.05). The proportion of carotid plaques in the observation group was significantly higher than that in the control group (χ2=27.833, P<0.001). Conclusion BPVSS indicates the severity of target organ damage in patients with hypertension. A greater BPV is correlated with a lower BPVSS score and more severe damages of the heart and blood vessels.