Acupuncture has been used to treat various disorders in China and some other eastern countries for thousands of years. Nowadays, acupuncture is gradually accepted as an alternative and complementary method in western countries for its undeniable therapeutic effects. However, its central mechanism is still unclear. It is especially difficult to reveal how different regions in the brain influence one another and how the relationship is among these regions responding to acupuncture treatment. Recently, by applying neuroimaging techniques and network theory, acupuncture studies can make further efforts to investigate the influence of acupuncture on regional cerebral functional connectivity (FC) and the modulation on "acupuncture-related" networks. Connectomics appears to be a new direction in research to further understand the central mechanism underlying acupuncture. In this paper, an overview of connectomics application in acupuncture research will be discussed, with special emphasis on present findings of acupuncture and its influence on cerebral FC. Firstly, the connectomics concept and its significance on acupuncture will be outlined. Secondly, the commonly used brain imaging techniques will be briefly introduced. Thirdly, the influence of acupuncture on FC will be discussed in greater detail. Finally, the possible direction in forthcoming research will be reviewed by analyzing the limitation of present studies.