As a world intangible cultural heritage, acupuncture is considered an essential modality of complementary and alternative therapy to Western medicine. Despite acupuncture's long history and public acceptance, how the cortical network is modulated by acupuncture remains largely unclear. Moreover, as the basic acupuncture unit for regulating the central nervous system, how the cortical network is modulated during acupuncture at the Hegu acupoint is mostly unclear. Here, multi-channel functional near-infrared spectroscopy (fNIRS) data were recorded from twenty healthy subjects for acupuncture manipulation, pre- and post-manipulation tactile controls, and pre- and post-acupuncture rest controls. Results showed that: (1) acupuncture manipulation caused significantly increased acupuncture behavioral performance compared with tactile controls. (2) The bilateral prefrontal cortex (PFC) and motor cortex were significantly inhibited during acupuncture manipulation than controls, which was evidenced by the decreased power of oxygenated hemoglobin (HbO) concentration. (3) The bilateral PFC's hemodynamic responses showed a positive correlation trend with acupuncture behavioral performance. (4) The network connections with bilateral PFC as nodes showed significantly increased functional connectivity during acupuncture manipulation compared with controls. (5) Meanwhile, the network's efficiency was improved by acupuncture manipulation, evidenced by the increased global efficiency and decreased shortest path length. Taken together, these results reveal that a cooperative PFC-Motor functional network could be modulated by acupuncture manipulation at the Hegu acupoint. This study provides neuroimaging evidence that explains acupuncture's neuromodulation effects on the cortical network.