Objective To investigate the clinical effect of repetitive transcranial magnetic stimulation (rTMS) in the treatment of Parkinson's disease (PD). Methods A total of 37 PD patients treated with drugs and rTMS (rTMS+drug group) and 45 PD patients treated with drugs alone (drug group) were enrolled, and motor symptoms (MS) and non-motor symptoms (NMS) were evaluated at baseline and at the end of two-year follow-up using Unified Parkinson's Disease Rating Scale III (UPDRS III) and Hoehn-Yahr (H-Y) staging, Non-Motor Symptom Questionnaire (NMSQ), Parkinson's Disease Sleep Scale (PDSS), Hamilton Depression Scale (HAMD), Hamilton Anxiety Scale (HAMA), and Mini-Mental State Examination (MMSE). Disease progression was analyzed and compared between the two groups. Results The rTMS+drug group had a significant increase in H-Y stage from baseline to the end of two-year follow-up (P<0.05), and the drug group had significant increases in the scores of UPDRS III, H-Y stage, HAMD, and HAMA and levodopa equivalent dose (LED) (P<0.05). Compared with the rTMS+drug group at the end of two-year follow-up, the drug group had significant increases in scores of UPDRS III, H-Y stage, and HAMD and LED (P<0.05). Conclusions Regular rTMS assisting conventional anti-PD drug therapy can delay the progression of PD, with a better clinical effect than drug therapy alone.