To investigate the effects of intermittent theta short burst pulse stimulation (iTBS) to the cerebellum vermis on lower limb motor dysfunction in stroke patients. Methods: A total of 42 stroke patients with post-stroke lower limb motor dysfunction were randomly divided into an iTBS group (21 cases) and a control group (21 cases). Both groups underwent standard rehabilitation training and physical therapy, with the iTBS group also receiving targeted iTBS to the cerebellar vermis for two weeks. The Fugl-Meyer assessment of Lower erxtremity (FMA-LE), 6-minute walking test, 60°/s concentric knee extension strength measurement, Berg Balance Scale (BBS), Modified Ashworth Scale (MAS) and Barthel Index (BI) were assessed before and after treatment in both groups. Results: There were no statistically significant differences in the FMA-LE, 6-minute walking test, 60°/s concentric knee extension strength measurement, BBS, MAS or BI scores between the two groups before treatment (P>0.05). After treatment, both groups showed significant improvements in the scores for the FMA-LE, 6-minute walking test, 60°/s concentric knee extension strength measurement, BBS, MAS and BI (P<0.05), whereas the iTBS group exhibited superior improvements in the FMA-LE, 60°/s concentric knee extension strength measurement, BBS and BI scores compared to the control group (P<0.05). Conclusion: iTBS targeting the cerebellar vermis can improve lower limb motor function and daily living abilities in stroke patients.