Brain is a complex nonlinear dynamic system consisting of related functional regions that can be described by the complex network model. Acupoint magnetic stimulation is an equivalent external stimulus for brain, which can be used as an important technical method to study the regulation mechanism of complex nervous system. It is of great significance to research the effect of acupoint magnetic stimulation on the structure and characteristics of brain functional network. Magnetic stimulation was applied to Neiguan (PC6) and the acquired EEG data were analyzed using dual-channel nonlinear method of mutual information in time domain. The corresponding brain functional networks before, during and after a magnetic stimulation were constructed and the characteristic parameters were studied based on the complex network theory. Results show that the average degree, average clustering coefficient and global efficiency of the brain functional network were increased under magnetic stimulation frequency of 3 Hz, while the average path length was reduced. The small world attribution of the corresponding functional network was enhanced, which made the information transfer among brain regions more efficiently. The brain functional networks under acupoint magnetic stimulation is studied for the first time as far as we know, which provides a new idea and approach to investigate the effect and regulation mechanism of transcutaneous acupoint magnetic stimulation to the complex nervous system.