Objective: To investigate the differential efficacy of deep brain stimulation (DBS) targeting distinct subthalamic nucleus (STN) subdivisions on Parkinson’s disease (PD) patients with refractory dysphagia, and to elucidate the potential remodeling mechanisms of brainstem swallowing-related nuclei. Methods: Seventy-six PD patients with dysphagia admitted between March 2020 and March 2023 were enrolled and randomly assigned to the sensorimotor subdivision group (n=38) or the limbic-associative subdivision group (n=38). Swallowing function was assessed preoperatively and at 12 and 24 months postoperatively using videofluoroscopic swallowing study (VFSS), high-resolution manometry, and the Penetration-Aspiration Scale (PAS). Tongue pressure and superior laryngeal nerve evoked potentials were also recorded. Results: At 24 months postoperatively, the PAS score in the sensorimotor group decreased from 5.89±1.12 preoperatively to 2.34±0.78 (P<0.01), which was significantly better than that in the limbic-associative group (4.12±0.95). VFSS revealed a 42.3% increase in laryngeal elevation amplitude and a 38.6% reduction in pharyngeal transit time following sensorimotor subdivision stimulation. Evoked potentials showed a 29.4% shortening of latency in the nucleus tractus solitarius, indicating enhanced excitability of brainstem swallowing interneurons. Conclusion: Precise targeting of the STN sensorimotor subdivision via DBS achieves long-term swallowing function remodeling by upregulating brainstem swallowing center excitability, offering a novel surgical strategy for PD-related dysphagia.