Objectives: To evaluate the efficiency of acupuncture at the acupoint of Bi’nao for hypophasis and the mechanisms responsible for effect in the cerebral cortex. Methods: Participants with hypophasis were selected from patients with incompletely recovered Bell’s palsy and randomly allocated into Bi’nao group, Sham Bi’nao group and healthy control group with 33 participants per group. Acupuncture therapy was applied at the real or sham Bi’nao acupoint to compare efficiency. Clinical effects were evaluated by the House-Brackman Scale (HBS), Eye Crack Width Measurement (ECWM) scale and Eyelid Strength Assessment (ESA) before and after therapy. Regions of the brain cortex that were stimulated by acupuncture were detected by task-state functional magnetic resonance imaging. Results: HBS and ESA scores in the Bi’nao group were lower than in the other two groups (P<0.05) while ECWM scores were higher (P<0.05). The cingulate cortex and cerebellum were activated during acupuncture stimulation in the Bi’nao group when compared to both the Sham Bi’nao group and the healthy control group (P<0.05). Conclusion: Acupuncture at the acupoint Bi’nao increased the recovery of hypophasis in patients with incomplete recovered Bell’s palsy. The underlying mechanism might be associated with the activation of the cingulate cortex and cerebellum.