A classic herbal formula Guizhi Fuling Wan (GFW) has been used for managing menopausal hot flushes (MHFs), but the evidence across different study types has not been systematically summarized. This project investigated the clinical effects, phytochemistry, pharmacodynamics, and potential mechanisms of actions of GFW on the causative target proteins potentially driving MHFs. Twenty English and Chinese databases were searched for relevant clinical and experimental studies. A total of 12,988 studies were identified, of which 46 were included. Seven clinical studies demonstrated GFW had no statistically significant changes in the frequency and severity of MHFs; however, it could improve peripheral blood flow in the fingertips, jaw, and toes. Thirty-five studies on phytochemistry identified 169 chemical compounds of GFW. Four experimental studies revealed GFW’s therapeutic effects (e.g., normalize calcitonin gene-related peptide [CGRP] level) and potential target protein/cytokine (estrogen receptor beta [ESR2] with genetic variation, CGRP receptor, and interleukin-8) on MHFs. Therapeutic effects across different study types were inconsistent, possibly due to the dose difference and genotype variety of ESR2 in the human population. Further clinical and experimental studies, as well as biochemical investigation on the mechanisms of actions of GFW, are recommended.