This research investigated the modulation of acupuncture at Quchi (LI11) on the brain activities in healthy individuals. Sub-bands power and EEG microstate analysis were carried out at pre-acupuncture, acupuncture, needle retaining and post-acupuncture periods in both the acupuncture group (n = 16) and control group (n = 18). Four microstate classes (A-D) were derived from the clustering procedure. Regression analysis was conducted, together with a two-way repeated measures ANOVA, which was then followed by Bonferroni correction. In the acupuncture group, we found the beta power during the acupuncture periods was significantly reduced. The channel-by-channel analysis revealed that acupuncture at LI11 mainly altered the power of delta, theta, and alpha waves in specific brain regions. The delta power increased predominantly in parietal, occipital, and central lobes, while theta and alpha power decreased predominantly in temporal, frontal, parietal, and occipital lobes. During the acupuncture period, participants in the acupuncture group showed a significant increase in both duration and contribution of microstate A, as well as the bidirectional transition probabilities A and B/D. Microstate analysis showed that acupuncture at LI11 significantly enhances the activity of microstate A and potentially strengthens the functional connectivity between the auditory network and either the visual network or the dorsal attention network. These correlational results indicate that acupuncture at LI11 mainly affects activities of the frontal, temporal, parietal, and occipital lobes. These findings highlight the potential of microstate as neuroimaging evidence and a specific index for elucidating the neuromodulatory effects of acupuncture at LI11.