Background: Carotid-femoral pulse wave velocity (cfPWV) and ejection duration (ED) have different impacts on target organ damage (TOD). The aim of this study was to determine the relationship of cfPWV and ED with TOD. Methods: A total of 1254 patients (64.27% males) from Ruijin Hospital were enrolled in this study from December 2018 to August 2022. Medical records, blood samples and urine samples were collected. The cfPWV was measured and ED was generated using SphygmoCor software (version 8.0, AtCor Medical, Sydney, Australia). TOD including left ventricular hypertrophy (LVH), microalbuminuria, chronic kidney disease (CKD), and abnormality of carotid intima-media thickness (CIMT) were evaluated. Results: Multiple stepwise linear regression models of cfPWV and ED (individually or together) showed that cfPWV was positively correlated with left ventricular mass index (LVMI) (\beta= 0.131, p = 0.002) and Log (albumin-creatinine ratio, ACR) (\beta= 0.123, p = 0.004), while ED was negatively correlated with LVMI (\beta= –0.244, p 0.001) and positively correlated with the estimated glomerular filtration rate (eGFR) (\beta= 0.115, p = 0.003). When cfPWV and ED were added separately or together in multiple stepwise logistic regression models, cfPWV was associated with CKD [odds ratio (OR) = 1.240, 95% confidence interval (CI) 1.055–1.458, p = 0.009], while ED was associated with LVH (OR = 0.983, 95% CI 0.975–0.992, p 0.001). In the control group with normal cfPWV and normal ED, LVH was significantly lower in patients with high ED (OR = 0.574, 95% CI 0.374–0.882, p = 0.011), but significantly elevated in those with high cfPWV and low ED (OR = 6.799, 95% CI 1.305–35.427, p = 0.023). Conclusions: cfPWV was more strongly associated with renal damage, while ED was more strongly associated with cardiac dysfunction. cfPWV and ED affect each other, and together have an effect on LVH.