Neuroimaging studies involving acute acupuncture manipulation have already demonstrated significant modulatory effects on wide limbic/paralimbic nuclei, subcortical gray structures and the neocortical system of the brain. Due to the sustained effect of acupuncture, however, knowledge on the organization of such large-scale cortical networks behind the active needle stimulation phase is lacking. In this study, we originally adopted a network model analysis from graph theory to evaluate the functional connectivity among multiple brain regions during the post-stimulus phase. Evidence from our findings clearly supported the existence of a large organized functional connectivity network related to acupuncture function in the resting brain. More importantly, acupuncture can change such a network into a functional state underlying both pain perception and modulation, which is exhibited by significant changes in the functional con-nectivity of some brain regions. This analysis may help us to better understand the long-lasting effects of acupuncture on brain function, as well as the potential benefits of clinical treatments.