To investigate the effects of intermittent theta burst stimulation (iTBS) of the cerebellum combined with conventional physical therapy on motor and balance functions in patients with hemiplegia following stroke. Methods: Forty stroke patients admitted to Beijing Fengtai You'anmen Hospital from May 2021 to December 2023 were selected and randomly divided into a control group and an experimental group, with 20 cases in each. Both groups received conventional pharmacological and rehabilitation treatments, while the experimental group received cerebellar iTBS prior to rehabilitation therapy, and the control group received sham stimulation. Motor and balance functions were assessed using the Berg Balance Scale (BBS), Fugl-Meyer Assessment (FMA), and the Modified Barthel Index (mBI) before treatment and two weeks after treatment. Diffusion Tensor Imaging (DTI) was performed to measure Fractional Anisotropy (FA) and Apparent Diffusion Coefficient (ADC) values of three pairs of cerebellar peduncles. Results: There was no statistically significant difference in BBS, FMA, and mBI scores between the two groups before treatment (P>0.05). After treatment, BBS, FMA, and mBI scores increased significantly in both groups (P<0.01), and the experimental group scored higher than the control group (P<0.05). Before treatment, there was no statistically significant difference in FA values of the cerebellar peduncles between the two groups (P>0.05). After treatment, there was no statistically significant difference in FA values of the affected-side cerebellar peduncles between the two groups (P>0.05), but the non-affected-side superior cerebellar peduncle FA value was higher in the experimental group than in the control group (P<0.05). Within the experimental group, the FA value of the non-affected-side superior cerebellar peduncle increased after treatment compared to before treatment (P<0.05). Within the control group, there was no statistically significant difference in FA values of the affected-side and non-affected-side cerebellar peduncles before and after treatment (P>0.05). After treatment, there was no statistically significant difference in ADC values of the cerebellar peduncles between the groups or between the affected-side and non-affected-side within groups (P>0.05). Conclusion: Cerebellar iTBS treatment can promote the recovery of motor and balance functions in patients with hemiplegia following stroke. The mechanism may be related to iTBS-induced cortical reorganization through the cerebellum, improving neural conduction ability and plasticity.