This study integrated neuroimaging and neurochemistry data to explore brain mechanisms in chronic insomnia disorder (CID) and the neuromodulatory effects of acupuncture. We analyzed a cross-sectional arterial spin labeling (ASL) dataset (N = 197) of CID patients and healthy controls to identify cerebral blood flow (CBF) changes. Additionally, a longitudinal ASL dataset (N = 44) examined CBF changes in CID patients after a 4-week acupuncture treatment or on a waitlist. We then assessed the impact of 19 neurotransmitter receptors/transporters on these CBF alterations. In cross-sectional comparisons, CID patients exhibited increased CBF in cortical areas and decreased CBF in subcortical regions, correlating with insomnia severity. In longitudinal comparisons, acupuncture treatment enhanced subcortical CBF and alleviated insomnia symptoms, changes not observed in the waitlist group. The left putamen was identified as an overlapping subcortical region involved in both CID-related changes and post-treatment alterations. Moreover, the CBF patterns induced by acupuncture negatively correlated with the abnormal patterns in CID patients, and both were significantly associated with GABAa and dopamine-D1 receptor densities. The observed decrease in CBF in the left putamen could potentially serve as a neural biomarker for CID, while acupuncture may alleviate insomnia symptoms by increasing CBF in this region, potentially through the modulation of GABAa and D1 receptor expressions.