Parkinson’s disease (PD) is a highly complex neurodegenerative disease, and its pathogenesis is influenced by DNA methylation, histone modification, and non-coding RNA. Research on Parkinson’s brain tissue and blood has shown that changes in DNA methylation/histone modification levels and variations in ncRNA and its target genes may trigger neurodegeneration changes in the brain and serve as potential non-invasive biomarkers for PD. Exercise can ameliorate the neurodegenerative diseases caused by aging and PD by reversing epigenetic changes. This article reviews the role of epigenetics in the pathogenesis of PD, explores the benefits of exercise, and provides a theoretical reference for research into improving PD by regulating epigenetics through exercise.