An accurate and continuous measurement of blood pressure (BP) is of great importance for the prognosis of some cardiovascular diseases in out-of-hospital settings. Pulse transit time (PTT) is a well-known cardiovascular parameter which is highly correlated with BP and has been widely applied in the estimation of continuous BP. However, due to the complexity of cardiovascular system, the accuracy of PTT-based BP estimation is still unsatisfactory. Recent studies indicate that, for the subjects before and after exercise, PTT can track the high-frequency BP oscillation (HF-BP) well, but is inadequate to follow the low-frequency BP variance (LF-BP). Unfortunately, the cause for this failure of PTT in LF-BP estimation is still unclear. Based on these previous researches, we investigated the cause behind this failure of PTT in LF-BP estimation. The heart rate- (HR-) related arterial baroreflex (ABR) model was introduced to analyze the failure of PTT in LF-BP estimation. Data from 42 healthy volunteers before and after exercise were collected to evaluate the correlation between the ABR sensitivity and the estimation error of PTT-based BP in LF and HF components. In the correlation plot, an obvious difference was observed between the LF and HF groups. The correlation coefficient r for the ABR sensitivity with the estimation error of systolic BP (SBP) and diastolic BP (DBP) in LF was 0.817 ± 0.038 and 0.757 ± 0.069, respectively. However, those correlation coefficient r for the ABR sensitivity with the estimation error of SBP and DBP in HF was only 0.403 ± 0.145 and 0.274 ± 0.154, respectively. These results indicated that there is an ABR-related complex LF autonomic regulation mechanism on BP, PTT, and HR, which influences the effect of PTT in LF-BP estimation.