BACKGROUND: Subthalamic deep brain stimulation (STN-DBS) has emerged for Parkinson's disease (PD), but its long-term effects on levodopa-induced dyskinesia (LID) remain poorly understood. OBJECTIVE: To assess the long-term LID outcomes and prognostic factors of STN-DBS. METHODS: A single-blind longitudinal cohort study was conducted in evaluating 84 PD patients with LID (mean age 61.89 years; 46.4% female; mean disease duration 10.30 years; and mean baseline levodopa-equivalent dose 854.16 mg/day) who underwent STN-DBS at Beijing Tiantan Hospital, Capital Medical University between 2019 and 2021. Assessments at baseline, 1-year (short-term), and 3-year (long-term) regarding motor symptoms, quality of life, neuropsychological status, and cognitive function were analyzed. Primary outcomes focused on LID symptoms (Unified Dyskinesia Rating Scale [UDysRS]). Multivariable linear regression identified prognostic factors. RESULTS: At 1-year, the UDysRS score improved significantly (74.4% reduction, P<0.001), with sustained but diminished benefits at 3-year (64.9% reduction vs baseline, P<0.001; 36.9% decline vs 1 year, P=0.012). The time and functional impact of LID also improved initially (62.5% and 64.3% reduction) but worsened over time (38.8% and 33.3% decline). Motor function and quality of life showed similar trends, while neuropsychological symptoms improved stably even after long-term follow-up; and cognitive function remained unchanged. Multivariable regression identified diphasic dyskinesia as a negative prognostic factor (short-term std.β=-0.296; long-term std.β=-0.239), whereas a higher levodopa-equivalent dose (short-term std.β=0.275; long-term std.β=0.261) and greater levodopa responsiveness (short-term std.β=0.215; long-term std.β=0.216) predicted better short- and long-term results. A longer disease duration correlated with worse long-term outcomes (std.β=-0.212). CONCLUSION: STN-DBS was associated with significant long-term improvements in LID, although the effectiveness gradually declined. The identified prognostic factors help in patient selection and counseling.