In recent years, with the increasing incidence of brain functional area tumors, the clinical application of functional area tumor resection has become extremely urgent. Intraoperative wake-up is an important auxiliary method of this operation, which can effectively reduce the damage of the brain function area caused by the operation and anesthesia itself while playing the role of auxiliary function area and tumor positioning. However, the intraoperative wake-up requires a higher anesthesia effect, so higher requirements are put forward for the choice of anesthetic drugs. Based on hemodynamic and serum molecular observations, this study found that dexmedetomidine- and etomidate-assisted anesthesia were used for intraoperative wake-up in brain functional area surgery, both of which could maintain hemodynamic stability. In addition, the arousal effect and brain protection of dexmedetomidine were better than those of etomidate, and the incidence of adverse reactions was lower during the arousal period. This can provide relevant reference for clinical improvement of the anesthesia effect and surgical safety of intraoperative wake-up.