This paper investigated the sustained effect of central nervous system activities on human brain between traditional manual acupuncture and electro-acupuncture on ST-36 by collecting resting-state functional magnetic resonance imaging (fMRI) data and analyzing the fMRI data. 12 (male/female=6/6, aged from 23 to 27) acupuncture naive, right-handed healthy adult volunteers were chosen and divided into manual acupuncture (MA) group (12 subjects) and electro-acupuncture (EA) group (12 subjects). The needle was rotated bi-directionally at the frequency of 2 Hz for 2 minutes stimulation on ST-36 during MA (2 Hz) and EA (constant square wave, 2 Hz, intensities ranging from 0.5 to 1.4 mA). Statistical results showed that manual acupuncture and electro-acupuncture induced different long-lasting responses after the administration of acupuncture on ST-36.Structures associated with the release of analgesia-related neurotransmitters, including the midbrain and basal ganglia, presented prolonged activities in post-stimulus stage. Different patterns of brain responses between the two modalities may show differences in the transmission channels of meridian and activities in neurotransmitter system.