Parkinson's disease (PD) is a devastating neurodegenerative disorder with growing prevalence worldwide and, as yet, no effective treatment. Drug repurposing promises to be invaluable for the identification of novel therapeutics for the treatment of PD due to the associated shortened drug development time, fewer safety concerns, and reduced costs. Here, we compiled gene expression data from 1,231 healthy human brains and 357 PD patients across ethnicities, brain regions, Braak stages, and disease status. By integrating them with multiple-source PD-associated genomic data, we found a conserved PD-associated gene co-expression module, and its alignment with the CMAP database successfully identified 15 drug candidates. Among these, we selected meclofenoxate hydrochloride (MH) and sodium phenylbutyrate (SP) for experimental validation because they are capable of passing through the blood brain barrier. In primary neurons, MH was found to prevent the neuronal death and synaptic damage associated with PD and to reverse the abnormal mitochondrial metabolism caused by PD. In hippocampal tissues, MH and SP were found to prevent the destruction of mitochondria, to reduce lipid peroxidation and to protect dopamine synthesis by PET-CT examination, malondialdehyde (MAD) testing and glutathione (GSH) testing, and immunohistochemical tests. Finally, MH was found to have the ability to improve gait behavior, and reduce anhedonic and depressive-like behaviors that are characteristics of PD mice. Taken together, our findings support the contention that MH may have the potential to ameliorate PD by improving mitochondrial metabolism and brain function.