Abstract: The therapeutic effectiveness of acupuncture has been proved by clinical practice. However, its effect mechanism is still unclear. Magnetic stimulation at acupuncture point provides a new way for studying the theory of acupuncture. In this study, a magnetic stimulation on Neiguan (PC6) acupoint was performed, and the corresponding EEG signals of quiescent and stimulated states were recorded. By using the feature of the non-linear dynamics (correlation dimension) and the mutual information method, brain functional networks were constructed and analyzed where the topology features of complex network were comparatively analyzed for the quiescent and stimulated states. The experimental results show that the topology of the network is changed and the connection of the network is enhanced. In additional, the efficiency of information transmission is also found improved and the "small-world" property tends to become stronger through stimulating PC6 acupoint.