To investigate the effects of acupuncture combined with rehabilitation training on the recovery of upper limb motor function in patients with acute ischemic stroke and to study brain function remodeling using functional magnetic resonance imaging (fMRI). Methods: Sixty acute ischemic stroke patients with motor dysfunction of the upper limbs were randomly divided into the treatment group and control group, with 30 patients in each. Patients in both groups were treated with routine drugs and exercise rehabilitation training for 3 months, and patients in the treatment group were additionally given acupuncture treatment. All patients were assessed before and after treatment by the NIHSS score, Fugl-Meyer assessment for upper extremity (FMA-UE), index finger tapping test, grip strength measurement, and exercise task-based fMRI scanning. Results: After treatment, the index finger tapping test, hand grip strength, NIHSS score, and FMA-UE score in both groups were improved compared with those before treatment (all P<0.01), and the degree of improvement in the treatment group was significantly higher than that in the control group (all P<0.01). Before treatment, both groups showed activation of the contralateral primary motor region (M1) and supplementary motor area (SMA) during gripping exercises; after treatment, both groups showed enhanced activation in the contralateral M1 and bilateral SMA (P<0.01) compared to before treatment, and the treatment group showed a greater enhancement than the control group (P<0.01). Conclusion: In acute ischemic stroke patients with upper limb motor dysfunction, acupuncture combined with rehabilitation is an effective treatment that can promote activation of the bilateral SMA and contralateral M1 and remodeling of brain function.