Object. To explore the specific effect of the international standard scalp acupuncture (ISSA) on patients with brain dysfunction after acute ischemic stroke (AIS) based on resting-state functional magnetic resonance imaging (Rs-fMRI). Design. A parallel-group randomized controlled trial. Participants. 30 hemiplegic patients with middle cerebral artery acute infarction of the dominant hemisphere. Interventions. 30 patients were divided into 2 groups randomly. 15 patients in the treatment group (TG) were treated with ISSA, needling at the parietal midline (MS5) and left anterior/posterior parietal-temporal oblique lines (MS6 and MS7), combined with western routine treatment. While another 15 patients in the control group (CG) received routine treatment only. Main Outcome Measures. (1) Functional connectivity (FC): patients received brain scan using 3.0 T MRI after the treatment for 1 week. Based on the Matlab2012a platform, SPM12 software and DPABI software were used to process the scanning data and finally the functional connectivity of the brain was obtained. (2) National Institute of Health Stroke Scale (NIHSS) score. Results. The difference in the NIHSS score between the two groups of patients before and after treatment was statistically significant (tNIHSS = 2.225; PNIHSS = 0.038), indicating that TG had a better effect. Centered to the seed region of the left supplementary motor area (SMA) (−5.32, 4.85, 61.38), FC increased at the left middle cerebellar peduncle, left cerebellum posterior lobe (uvula and declive), vermis, fusiform gyrus, lingual gyrus, inferior occipital gyrus, calcarine, cuneus, precuneus, BA7, BA18 and BA19, etc. Centered to the seed region of the left parahippocampal gyrus (PG) (−21.17, −15.95, −20.70), FC increased at the left precuneus, inside-paracingulate, inferior parietal gyrus, paracentral lobule, BA5, BA6, BA7, and BA40, right median cingulate, precuneus, BA19, BA23, and BA31, etc. Conclusions. It is indicated that ISSA can regulate the brain functional connection in patients with middle cerebral artery acute infarction in the dominant hemisphere and specifically strengthen the connections between visual, cognitive, motor control, and planning-related brain regions, which may be related to the recovery of movement in the mechanism. This trial is registered with ChiCTR-IOR-15007672.