Acupuncture is a clinical intervention consisting of multiple stimulus components, including somatosensory stimulation and manipulation of therapeutic context. Existing findings in neuroscience consolidated cognitive modulation to somatosensory afferent process, which could differ from placebo mechanism in brain. Here, we aimed to identify intrinsic process of brain interactions induced by compound stimulus of acupuncture treatment. To separately and comprehensively investigate somatosensory afferent and cognitive/affective processes in brain, we implemented a novel experimental protocol of contextual manipulation with somatosensory stimulation (real acupuncture: REAL) and only contextual manipulation (phantom acupuncture: PHNT) for fMRI scan, and conducted independent component (IC)-wise assessment with the concatenated fMRI data. By our double (experimentally and analytically) dissociation, two ICs (CA1: executive control, CA2: goal-directed sensory process) for cognitive/affective modulation (associated with both REAL and PHNT) and other two ICs (SA1: interoceptive attention and motor-reaction, SA2: somatosensory representation) for somatosensory afference (associated with only REAL) were identified. Moreover, coupling between SA1 and SA2 was associated with a decreased heart rate during stimulation, whereas CA1 was associated with a delayed heart rate decrease post-stimulation. Furthermore, partial correlation network for these components demonstrated a bi-directional interaction between CA1 and SA1/SA2, suggesting the cognitive modulation to somatosensory process. The expectation for the treatment negatively affected CA1 but positively affected SA1 in REAL, whereas the expectation positively affected CA1 in PHNT. These specific cognitive-somatosensory interaction in REAL were differed from vicarious sensation mechanism in PHNT; and might be associated with a characteristic of acupuncture, which induces voluntary attention for interoception. Our findings on brain interactions in acupuncture treatment elucidated the underlying brain mechanisms for compound stimulus of somatosensory afferent and therapeutic contextual manipulation, which might be a specific response to acupuncture.