Objective To explore the application of serum procalcitonin (PCT), NT-proBNP and Transcranial Doppler (TCD) in monitoring sepsis related encephalopathy (SAE) and its predictive value for its prognosis. Methods The 148 patients with sepsis treated in our hospital from January 2020 to April 2022 were selected as the research objects. According to whether SAE was combined or not, they were divided into SAE group (67 cases) and non SAE group (81 cases). Serum PCT and NT-proBNP levels were measured by immunoluminescence assay and enzyme-linked immunosorbent assay respectively. Peak systolic blood flow velocity (VS), end diastolic blood flow velocity (VD), mean blood flow velocity (VM) and resistance index (RI) were measured by TCD. The 30 day prognosis of SAE patients was recorded. The poor prognosis was based on the progress of the patient′s condition or death, otherwise, it was a good prognosis. Results SAE group APACHE Ⅱ was score higher than non SAE group (P＜0.05). SAE group serum PCT and NT-proBNP were higher than non SAE group (P＜0.05). SAE group Vs, Vd and Vm of patients were lower than non SAE group, while RI of patients was higher than non SAE group (P＜0.05). The poor prognosis serum PCT and NT-proBNP in patients were higher than good prognosis (P＜0.05). The poor prognosis Vs, Vd and Vm of patients were lower than patients with good prognosis, while the RI of patients with poor prognosis was higher than patients with good prognosis (P＜0.05). The sensitivity and specificity of PCT in SAE diagnosis were 82. 13% and 95. 12% respectively. The sensitivity and specificity of NT proBNP were 98. 52% and 97. 51%, respectively. Conclusion The levels of serum PCT and NT-proBNP in patients with SAE are increased, and there are abnormal cerebral hemodynamics, which are closely related to the prognosis, it can be used as a reference index to predict the patients with SAE and their prognosis