Objective To explore the possible mechanism of high-frequency repetitive transcranial magnetic stimulation （HF-rTMS） on limb function in patients with ischemic stroke （IS） from the perspectives of activation of the brain's motor cortex and serum biomarkers ［thrombomodulin （TM）， vascular cell adhesion molecule-1 （VCAM-1）］. Methods A total of 136 patients with ischemic stroke （IS） who were admitted to the hospital from January 2023 to May 2025 were randomly assigned to four groups using the random-number table method： the combined group （n = 34， receiving high - frequency repetitive transcranial magnetic stimulation （HF-rTMS） plus butylphthalide）， the HF-rTMS group （n = 34， receiving HF-rTMS）， the butylphthalide group （n = 34， receiving butylphthalide）， and the control group （n = 34， receiving conventional drugs and rehabilitation training intervention）. The treatment duration was 28 days.Comparisons were made among the four groups regarding neurological functions ［assessed by the National Institutes of Health Stroke Scale （NIHSS）］， serum markers ［including serum S100β， brain-derived neurotrophic factor （BDNF）， and neuron-specific enolase （NSE）］， motor cortex activation of the brain ［evaluated by the latency/amplitude of motor evoked potential （MEP） and central motor conduction time （CMCT）］， limb functions ［assessed by the Brunnstrom stage and Fugl-Meyer Assessment （FMA） score］， Berg Balance Scale （BBS） score， modified Barthel index （MBI） score， and serum levels of thrombomodulin （TM） and vascular cell adhesion molecule-1 （VCAM-1） before treatment and 28 days after treatment.The treatment safety of the four groups was evaluated. Pearson correlation analysis was used to analyze the relationship between changes in FMA scores and changes in related indicators. Results After treatment， the NIHSS score， MEP latency， CMCT， and the levels of serum S100β， NSE， TM， and VCAM-1 in the combined group were lower than those in the HF-rTMS group， the butylphthalide group， and the control group （P < 0.05）. In contrast， the MEP amplitude， FMA， BBS， MBI scores， and the serum BDNF level were higher （P < 0.05）. There were no statistically significant differences in the above-mentioned indicators between the butylphthalide group and the HF-rTMS group （P > 0.05）. There was no statistically significant difference in the incidence of adverse reactions among the four groups （P > 0.05）. The increase in the total FMA score of IS patients after treatment was positively correlated with the increase in the amplitudes of MEP （P < 0.001） and negatively correlated with the decrease in the levels of serum TM and VCAM-1 （P < 0.001）. Conclusions The combination of HF-rTMS and butylphthalide can more effectively restore the neurological function of patients with IS， and promote the improvement of their limb function， balance， and activities of daily living. The synergistic activation of the brain's motor cortex and the down-regulation of serum TM and VCAM-1 levels may serve as its mechanism of action.