This study aimed to explore the clinical effects of intervention with Lycium ruthenicum Murr. (LR) and Lycium barbarum L. (LB) on PD patients, reveal the mechanism by which gut microbiota is involved in the overall metabolism of PD patients. The study examined the effects of LR and LB intake on intestinal microflora, serum/urine metabolites, and the Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) in 30 PD patients enrolled and randomized into 3 groups. Each received 16 g LR daily or 16 g LB daily or blank control for 6 months. The study found that LR and LB intervention reduced the MDS-UPDRS Ⅰ score and MDS-UPDRS Ⅳ score, although not statistically significant. The abundance of Bacteroides increased and the abundance of Flavobacteriaceae in the LR group decreased compared to the control group. LR may regulate the glycerophospholipid metabolism pathway, and α-linolenic acid metabolism pathway to slow down the progress of PD. After LB intervention, the abundance of Lachnoclostridium increased, the abundance of Blautia, norank_f__Eubacterium_coprostanoligenes_group, Bifidobacterium, Coprococcus and norank_f__Lachnospiraceae decreased in the LB group, and compared to the control group, the abundance of Agathobacter increased, the abundance of Lachnospiraceae and Flavobacteriaceae decreased. The results showed that LB may improve PD symptoms by regulating glycine, serine and threonine metabolism pathways, sphingolipid metabolism pathways, and starch and sucrose metabolism pathways. This study provides evidence support for LR and LB as medicinal and food homologous functional foods to improve PD disorders.