Acupuncture's actions have been explained by biomedical research. However, the meridian system used in acupuncture needs further clarification. This review describes how acupuncture affects the body and brain. From the perspective of traditional East Asian medicine, the meridian system is closely connected with acupuncture's treatment effects. In the body, the indications of acupoints, primarily established based on the meridian system, have spatial symptom patterns. Spatial patterns of acupoint indications are distant from the stimulated sites and strongly associated with the corresponding meridian's route. Understanding how acupuncture works based on the original meridian system is important. From a neuroscience perspective, an acupuncture-induced sensation originates from the bottom-up action of simple needling in the peripheral receptor and the reciprocal interaction with top-down brain modulation. In the brain, enhanced bodily attention triggered by acupuncture stimulation can activate the salience network and deactivate the default mode network regardless of the actual stimulation. The application of data science technology to acupuncture research may provide new tools to uncover the principles of acupoint selection and enhance the clinical efficacy of acupuncture treatment in various diseases.