Objective A case-control study was conducted to explore the effect of acupuncture combined with rehabilitation training on limb function and nerve injury rehabilitation in elderly patients with stroke. Methods A total of 72 elderly patients with stroke treated from March 2019 to June 2021 in our hospital were enrolled as the object of study. The clinical data were collected and divided into two groups according to their different treatment methods. The patients cured with routine treatment combined with rehabilitation training were taken as the control group and the patients cured with acupuncture combined with rehabilitation training as the study group. The clinical efficacy was recorded, and the cognition and activities of daily living were evaluated by Terrell Cognitive Assessment scale, limb motor function score, and activities of daily living scale. The National Institutes of Health Stroke Scale (NIHSS) and Glasgow Coma Scale (GCS) were employed to compare the neurological function before and after treatment. Glasgow Outcome Scale (GOS) and Disability Rating Scale (DRS) were adopted to evaluate the functional prognosis. The simplified Fugl-Meyer assessment of motor recovery score was employed to evaluate the limb function of the patients. The Wolf Motor Function Test (WMFT) score was adopted to evaluate the functional rehabilitation effect of the patients. Enzyme-linked immunosorbent assay (ELISA) was adopted to determine the serum neurological function indexes such as nerve growth factor, Smur100B protein, and glial fibrillary acidic protein. The cerebral blood flow (CBF), peak time, average transit time, and cerebral blood volume were measured by CT perfusion imaging, and the incidence of side effects during treatment was recorded. Results Regarding the recovery of cognitive function and daily function after treatment, after treatment, the MoCA and ADL scores were increased, and the comparison indicated that the MoCA and ADL scores of the study group were remarkably higher compared to the control group (P < 0.05). With regard to the FMA-UE scores after treatment, the Fugl-Meyer scores were gradually increased, and the Fugl-Meyer scores in the study group were remarkably higher compared to the control group (P < 0.05) in the next two months. After 2 weeks, 4 weeks, 6 weeks, and 6 weeks of treatment, the WMFT scores gradually increased, and the WMFT score of the study group was remarkably higher compared to the control group. After treatment, the levels of nerve growth factor and S-100B protein were decreased, and the level of glial fibrillary acidic protein was increased. Comparison between the two groups, it indicated the improvement degree of each neurological function index in the study group was remarkably better (P < 0.05). With regard to cerebral hemodynamic indexes after treatment, 1 week after treatment, the CBF and average transit time of the observation group were remarkably higher compared to the control group, and the levels of cerebral blood volume and peak time were remarkably lower compared to the control group (P < 0.05). After 4 weeks of treatment, the cerebral hemodynamic indexes of the observation group did not change remarkably, and they were all lower than 1 week after the treatment. In the terms of side effects, 1 case of limb dysfunction, 1 case of swallowing dysfunction, 1 case of electrolyte disturbance, and none of infection in the study group, the incidence of adverse reactions was 8.33%. In the control group, there were 3 cases of limb dysfunction, 2 cases of swallowing dysfunction, 2 cases of electrolyte disturbance, and 3 cases of infection, and the incidence of adverse reactions was 27.78%. Compared between groups, the incidence of adverse reactions in the study group was lower (P < 0.05). Conclusion Early use of acupuncture combined with rehabilitation training has a remarkable therapeutic effect on elderly stroke patients. It can remarkably promote the recovery of the patient's condition, remarkably enhance their neurological function, cognitive function, motor function, and daily life function, and effectively strengthen the patient's prognosis score. It has important clinical application value to reduce the incidence of adverse reactions.