Magnetic stimulation is a non-invasive and almost painless technique and has been used to modulate nerve activities, treat disorders and maintain health, just like acupuncture. Acupuncture point (acupoint) is a specific point in human body with high sensitivity to acupuncture treatment. In this paper, magnetic stimulation was used to stimulate Neiguan (PC6) acupoint. 64-channel EEG signals in three stages (before, during and after magnetic stimulation) were recorded to determine whether magnetic stimulation at PC6 acupoint might modulate ongoing EEG or not and whether specific cerebral cortex areas would be activated. C0 complexity of EEG signals was analyzed. The statistical analysis results showed that the parietal lobe of cerebral cortex covered by P1, PZ and P2 electrodes was activated during magnetic stimulation at PC6 acupoint, temporal lobe and parietal-occipital lobe covered by T7, P5, PO7, PO5 electrodes were activated after magnetic stimulation. It suggested that magnetic stimulation at PC6 acupoint would activate specific cerebral cortex areas.