Extract of Acanthopanax senticosus harms (EAS) has been shown to have neuroprotective effects on Parkinson's disease (PD) cell model against α-synuclein overexpression and toxicity. However, studies of its anti-PD mechanism are challenging, owing to the complex pathophysiology of PD, and complexity of EAS with multiple constituents acting on different proteomic pathways. Here, we have investigated the proteomic profiles and potential biomarkers in a cell model of A53T mutant α-synuclein (A53T-α-Syn) overexpression after treatment of EAS. Using an iTRAQ (isobaric tags for relative and absolute quantitation)-based proteomics research approach, we identified 3425 modulated proteins, out of which 84 were found to be altered by A53T-α-Syn and considered as potential biomarkers. After treatment with EAS, the group showed the tendency to correct the abnormal expressions of 16 proteins out of 84 potential biomarkers, which were associated with the formation of Lewy body, mitochondrial energy metabolism, protein synthesis and apoptosis, etc. This study indicated that EAS might be a promising candidate for prevention or treatment of PD by regulating the related proteomic pathways in A53T-α-Syn transgenic SH-SY5Y cells.