Bell's palsy (BP), an idiopathic and unilateral facial paralysis, is frequently treated by acupuncture in Asia. This study aims to investigate the connectivity changes of the primary somatosensory cortex (SI) induced by acupuncturing at ipsilateral and contralateral Hegu acupoints of BP patients. Fifteen healthy volunteers and thirty BP patients were recruited, who underwent the restingstate functional MRI scanning before and after acupuncture. All subjects received acupuncture treatment at either ipsilateral or contralateral Hegu acupoint. Functional connectivity of bilateral SI was calculated for further intergroup analysis. The results showed significant functional connectivity alterations in the contralateral acupoint group (P<0.01) while no significant alterations were observed in neither the ipsilateral acupoint groups nor the healthy control groups. For the SI connectivity alteration, a significant difference was observed between the contralateral group and the ipsilateral group (P<0.01). These results suggested that acupuncturing at the contralateral and ipsilateral Hegu acupoint could induce different alterations in functional connectivity in recovery from BP. Therefore, the recovery mechanism of acupuncturing might vary from side to side.