Background: Brain plasticity and functional reorganization are the main mechanisms of stroke rehabilitation and the theoretical basis for transcranial magnetic therapy. Bimodal balance recovery model suggests that the structural integrity of neural pathways affects the functional reorganization mode of brain recovery after stroke. The principal neural pathway that innervates swallowing is the corticobulbar tract (CBT). The goal is to investigate the impact of corticobulbar tract integrity on swallowing function recovery in post-stroke dysphagia (PSD) patients treated with repetitive transcranial magnetic stimulation (rTMS). Methods: Thirty-five patients with high CBT integrity (relative fractional anisotropy (rFA) >0.5) and 32 patients with low CBT integrity (rFA \le0.5) were respectively assigned to three subgroups through a random number table: 5 Hz frequency rTMS group, 1 Hz frequency rTMS group, and Sham rTMS group. The Standardized Swallowing Assessment (SSA), Penetration Aspiration Scale (PAS), and Dysphagia Outcome Severity Scale (DOSS) were analyzed before and after therapy. Results: Significant improvements in SSA (p 0.05), PAS (p 0.05), and DOSS scores (p 0.05) were seen in the high frequency (HF) and low frequency (LF) groups compared with the Sham group for patients with high CBT integrity. Increased SSA (p 0.05), PAS (p 0.05), and DOSS scores (p 0.05) demonstrated that the HF group achieved greater remediation than the LF and Sham groups for patients with low CBT integrity. Conclusions: Both 5 Hz and 1 Hz rTMS over the contralateral hemisphere are effective for the treatment of swallowing disorders for patients with high CBT integrity after stroke; 5 Hz rTMS over the contralateral hemisphere is more effective than 1 Hz and sham stimulation for patients with low CBT integrity.