Cerebral Stroke is an acute cerebrovascular disease, a disease of brain tissue damage caused by the sudden rupture or blockage of blood vessels in the brain that prevents blood flow to the brain. Acupuncture has become a popular treatment for stroke, with auricular acupuncture providing a new idea for stroke treatment. However, the neuromodulatory mechanism of auricular acupuncture in the brain is still unclear. The aim of this study was to investigate the effect of auricular acupuncture in the treatment of upper limb dysfunction and the activation of specific brain regions in stroke patients. Forty patients with stroke hemiplegia who met the nerf criteria were included in the experiment and randomly assigned into two groups (20 patients in each group): the auricular acupuncture group and the control group. Fugl-Meyer score (FMA) assessment of upper limb motor function, motor evoked potential (MEP) measurement, and functional near-infrared brain function imaging (fNIRS) data acquisition in the primary motor M1 area of the brain at rest were performed before and after treatment, respectively. It was found that: 1) after auricular acupuncture treatment, the patients in the auricular acupuncture group showed significantly greater peak MEP and significantly higher oxyhemoglobin content in the M1 region of the brain compared with the control group, with a significant activation effect (MEP: P-value = 0.032, t = -2.22; HbO2; f = 4.225, p = 0.046); 2) in the clinical efficacy assessment, the FMA score in the auricular acupuncture group after treatment (p = 0.0122, t = 2.769). The results suggest that auricular acupuncture has an ameliorative effect on upper limb motor deficits after stroke and that activation of the M1 region of the brain may be a key node in auricular acupuncture for treating upper limb dysfunction in stroke patients, a finding that emphasizes the potential for clinical application of auricular acupuncture therapy for stroke patients with potential mechanisms influencing the outcome.