Objective: To explore the efficacy of repetitive transcranial magnetic stimulation (rTMS) combined with isokinetic muscle strength training in the treatment of hemiplegic function in patients during the recovery period of stroke. Method: 144 hemiplegic patients in the recovery period of stroke who were treated in our hospital from March 2023 to August 2025 were selected as the research subjects. The patients were divided into the control group (n=72) and the observation group (n=72 cases) by the random number table method. The control group received rTMS+ conventional rehabilitation treatment. The observation group received rTMS+ isokinetic muscle strength training. Both groups were continuously intervened for 8 weeks. The neuroelectrophysiological indicators [motor evoked potential (MEP), surface electromyography (sEMG), MEP latency, amplitude, and integrated electromyography value (iEMG)], motor function indicators [FMA scale, modified Ashworth scale (MAS)], activities of daily living [Barthel index (BI)] and clinical efficacy of the two groups were analyzed and compared. Result: Compared with before treatment, the MEP latency of the upper and lower limbs in both groups after treatment was significantly reduced, and the MEP amplitudes of the upper and lower limbs and the sEMG-iEMG values of the biceps brachii and quadriceps femoris were significantly increased. Moreover, the improvement amplitudes of various neuroelectrophysiological indicators in the observation group were significantly greater than those in the control group (P<0.05). After treatment, the total FMA scores and upper and lower limb scores of both groups were significantly increased compared with those before treatment, and the MAS scores were significantly decreased compared with those before treatment. Moreover, the variation ranges of the total FMA score, FMA upper limb score, FMA lower limb score and MAS score in the observation group were significantly greater than those in the control group (P<0.05). After treatment, the BI scores of both groups were significantly higher than those before treatment, and the BI score of the observation group after treatment was significantly higher than that of the control group (P<0.05). The total effective rate of treatment in the observation group was significantly higher than that in the control group (P<0.05). There was no significant difference in the incidence of adverse reactions between the two groups (P>0.05). Conclusion: rTMS combined with isometric muscle strength training can synergistically improve the motor function of hemiplegic patients in the recovery period of stroke, relieve muscle spasm, enhance the ability of daily living, strengthen muscle strength and promote the recovery of nerve conduction function, and has relatively high safety.