Parkinson’s disease is a degenerative disease of the central nervous system, and it occurs in middle-aged and elderly people. Studies have shown that both the clinical symptoms and neuropathological evidence of Parkinson’s disease suggest that Parkinson’s disease may originate in the gut. Intestinal flora homeostasis plays an important role in maintaining normal functions of the brain and nervous system. It participates in changes in cellular flora through oxidative stress, inflammatory response, and immune response during metabolism. Intestinal flora disorders are closely related to the onset of neurological diseases such as Parkinson’s disease (PD). In order to better understand the relationship between intestinal flora and Parkinson’s disease, this article studies the correlation between PD rat models and intestinal flora, and analyzes the possible relationship between them. The 6-OHDA PD rat model is currently a better model preparation method, which is widely used in PD research. The experimental results show that using Fe3O4 nanoparticle technology to detect intestinal flora disorders in PD patients, and the role of intestinal flora disorders in Parkinson’s disease may include affecting inflammatory response and oxidative stress, α-synuclein Protein (α-syn), these modes of action are not independent, there are complex and synergistic effects, and the molecular simulation mechanism may play a key role in these effects. There is a certain relationship between intestinal flora and Parkinson’s disease, but the specific mechanism is not clear, and further research is needed to provide more directions for the early diagnosis and early treatment of PD.