Postural orthostatic tachycardia syndrome (POTS) presents excessive orthostatic tachycardia and orthostatic intolerance. POTS is a common and therapeutically challenging condition affecting numerous people worldwide. As many disease entities can be confused with POTS, it becomes critical to identify this syndrome. Moreover, unbalanced autonomic nervous activity can induce cardiovascular diseases and influence the bio-feedback mechanism: Baroreflex (BR) and cerebral autoregulation (CA). BR and CA are important bio-mechanisms that maintain a stable circulatory system via the autonomic nervous system. Therefore, an impaired autonomic nervous system would lead to imbalanced BRS and CA. Consequently, we propose an advanced cross-correlation function (ACCF) time-domain approach to analyze baroreflex and cerebral autoregulation using physiological signals. This study assesses relation changes in BR and CA using ACCF in POTS for early clinical detection and diagnosis. The ACCF analysis results has thresholds that reveal that the BR of healthy and POTS groups present significantly different maximum CCF values (p < 0.05). The complete CCF index shows that the BR phase changes significantly into phase lag in the POTS group. Although CA analysis using the maximum CCF index was mildly weak, it did not differ in the POTS group. Thus, POTS only affects BR. An increasing sympathetic activity might induce an unbalanced baroreflex effect and increase cerebral vasomotor tone with CA. Maximum CCF value correlation coefficients between BR and CA indicated positive in POTS groups and negative in the healthy group. It could be speculated that the sympathetic nervous system compensates to improve BR function, which remains CA function. The advantage of this ACCF algorithm is that it helps observe BR and CA for early detection.