This study investigated the hemodynamic response of peripheral ultrasound signals in coronary artery disease (CAD) patients using transfer function (TF) characteristic analysis before, during and immediately after enhanced external counterpulsation (EECP) therapy. Fifty-eight CAD patients and sixty-two controls (N = 120) all received a single, 45-min EECP session. Blood flow ultrasound signals in the carotid and brachial arteries were acquired and spectrum curves were extracted and used to establish ARX model. TF characteristics (coefficients (A, B); Zeros (zx, zy); Poles (px, py)) were analyzed and compared between CAD and control groups across all phases. Additionally, multiple TF characteristics were integrated by linear combination to construct a CAD indicator. The classification accuracy of TF characteristics during and immediately after EECP are significantly higher than time-domain (p = 0.03) and frequency-domain features (p = 0.004). Immediately after EECP, coefficient features displayed the most significant changes in control groups, while Zero and Pole features were most significant in CAD patients. Multiple TF characteristics exhibited greater differences immediately after EECP compared to before and during EECP. This study demonstrates that both single and multiple TF characteristics provided the most distinct response between groups immediately after EECP. This study highlights the potential of TF analysis of peripheral ultrasound for non-invasive assessment of therapy in CAD patients.