Objective To investigate the effects of low-frequency repetitive transcranial magnetic stimulation (rTMS) and contralaterally controlled functional electrical stimulation (CCFES) on promoting the recovery of hand dysfunction and the influence on cerebral cortical function in elderly hemiplegic stroke patients. Methods A total of 150 elderly hemiplegic stroke patients with hand dysfunction admitted to Handan First Hospital from January 2024 to January 2025 were enrolled as study subjects. According to the rehabilitation treatment methods, they were divided into a CCFES group (CCFES + conventional rehabilitation training) and a combination group (CCFES+rTMS+conventional rehabilitation training). Before and after treatment, Wolf motor function test (WMFT) was used for evaluation of upper limb function of the affected side, and simplified Fugl-Meyer assessment (FMA) for evaluation of motor function of the affected side, and modified ashworth scale (MAS) for degree of wrist spasm on the affected side. The wrist active range of motion (AROM) was measured, and modified Barthel index (BI) was employed to assess the daily living ability of patients. Meanwhile, a magnetic stimulator was used to measure the resting motor threshold (RMT), motor evoked potential (MEP) cortical latency, MEP amplitude, and corresponding interhemispheric asymmetry (IHA) index in both the affected and healthy hemispheres. SPSS 26.0 was used for statistical analysis. Comparisons between the two groups was performed using t test or χ² test depending on data type. Results After treatment, the WMFT score, FMA score, BI, and AROM in wrist dorsiflexion, palmar flexion, radial deviation, and ulnar deviation in both groups increased compared with those before treatment in the same group, and the above indicators in the combination group were higher than those in the CCFES group, with statistically significant differences (all P<0.05). After treatment, the wrist spasm degree MAS score in both groups decreased compared with that before treatment, and the MAS score in the combination group was lower than that in the CCFES group, with statistically significant differences (all P<0.05). After treatment, the RME, IHARMT, MEP cortical latency, IHA latency and IHA amplitude levels of the affected side in both groups decreased compared with those before treatment in the same group, and the above indicators in the combination group were lower than those in the CCFES group, with statistically significant differences (all P<0.05). After treatment, the RME of the healthy side and MEP amplitude of the affected side in both groups increased compared with those before treatment in the same group, and the RME of the healthy side and the MEP amplitude of the affected side in the combination group were higher than those in the CCFES group, with statistically significant differences (all P<0.05). Conclusion CCFES combined with rTMS can further enhance the recovery of hand function in elderly hemiplegic stroke patients, and improve the imbalance between bilateral cerebral hemispheres after stroke, and it has high therapeutic safety and good clinical application value.