Abstract Background Parkinson’s disease (PD) is a progressive neurodegenerative disease common in aged populations. Classified by Hoehn & Yahr stages, patients are often divided into mild/early stage, moderate/middle stage, and advanced/late stage. With disease progression, PD shows high heterogeneity in each stage. Based on traditional Chinese medicine (TCM) syndrome differentiation theory and our previous works, we found that during the early stage, the main syndrome is Yin deficiency of the liver and kidney; during the moderate stage, the main syndromes are phlegm heat and wind stirring and blood stasis and wind stirring; and during the late stage, the dominant syndromes are deficiency of Yin and Yang and deficiency of Qi and blood. Hence, we proposed a new model of TCM treatment by the stage of PD. Based on Shudi Pingchan formula, an experimental formula of our team, we developed Ziyin Pingchan formula, Jiedu Pingchan formula, and Fuzheng Pingchan formula to treat each stage. This study is designed to evaluate the therapeutic effect of treating Parkinson’s disease by stages using traditional Chinese medicine and to provide an evidence base for forming a standardized scheme of diagnosis and treatment. Methods This study is designed as a multicentre, randomized, double-blind, placebo-controlled clinical trial. Patients will be stratified into 3 subgroups according to Hoehn & Yahr stage; 172, 168, and 72 participants will be required to be in the mild PD, moderate PD, and advanced PD subgroups, respectively, and will be randomized into the treatment or control group at a 1:1 ratio. The mild PD subgroup will receive a 48-week intervention, and the other 2 groups will receive a 24-week intervention. All groups will have a follow-up visit 12 weeks after starting the intervention. The intervention group will receive the Ziyin Pingchan formula, Jiedu Pingchan formula, or Fuzheng Pingchan formula, and the control group will receive the corresponding placebo. The primary outcomes will be the first addition of levodopa for the mild PD subgroup, the duration of the “OFF” period for the moderate PD subgroup, and the Parkinson's Disease Questionnaire (PDQ-39) for the advanced PD subgroup. The secondary outcomes will also be verified by subgroups, including the Unified Parkinson’s Disease Rating Scale (UPDRS), Parkinson’s Disease Sleep Scale-2 (PDSS-2), scales for Outcomes in Parkinson’s Disease—Autonomic (SCOPA-AUT), and the nonmotor symptom scale (NMSS). Expected outcomes To our knowledge, this is the first trial to combine TCM syndrome differentiation with PD clinical stages and put it into clinical practice. The results of this trial will provide clinical evidence for the therapeutic effect of TCM formulas on PD patients of all stages and help build a new TCM treatment by stage model of PD. Trial registration: This trial is registered at the Chinese Clinical Trial Registry ( http://www.chictr.org.cn/ ). Registration number: ChiCTR2200056373, Date: 2022–02-04, version 1.