Traditional Chinese Medicine (TCM), as a complex medical science which reflects philosophical principles and embodies large dialectical thought, is used to place the human body into a large system for observation. Acupuncture as a vital part of TCM, has been practiced to treat various diseases and symptoms. However, acupuncture is also facing severe challenges resulted from insufficient modern scientific research. Nowadays, the holistic effects of acupuncture can be researched by some modern approaches, such as the systems biology and fMRI technique. It is believed that having a better understand will greatly promote acupuncture research and be beneficial to scientization and modernization of acupuncture.