This study was designed to investigate the relationship between heart-carotid pulse wave velocity (hcPWV) and carotid intima-media thickness (CIMT) in hypertensive patients, and also to examine the effect of pre-ejection period (PEP) on it. Doppler ultrasound device was used to measure CIMT in left common carotid artery. Hypertensive patients were divided into normal (n = 36, CIMT ≤0.8 mm) and thickened (n = 31, CIMT > 0.8 mm) group. Electrocardiogram R-wave-based carotid pulse wave velocity (rcPWV) and aortic valve-carotid pulse wave velocity (acPWV) were calculated as the ratio of the travel length to the pulse transit time with or without PEP, respectively. CIMT has significant relations with rcPWV (r = 0.611, P < 0.0001) and acPWV (r = 0.384, P = 0.033) in thickened group. Moreover, CIMT showed stronger correlation with rcPWV than with acPWV in thickened group. Furthermore, both acPWV and rcPWV were determinant factors of CIMT in thickened group, independent of clinical confounders including age, gender, smoking behavior, systolic blood pressure, diastolic blood pressure, fasting blood glucose, total cholesterol, high-density lipoprotein cholesterol, antihypertensive medication, and plaque occurrence. However, similar results were not found in normal group. Since CIMT has been considered as an index of atherosclerosis, our results suggested that both rcPWV and acPWV could be useful indexes of atherosclerosis in thickened CIMT hypertensive patients. Additionally, if hcPWV is computed with heart-carotid pulse transit time, including PEP could improve the accuracy of atherosclerosis assessment in hypertensive patients.