Background: Neuroinflammation plays a vital role in the pathology of Parkinson’s disease (PD). Eupatorium lindleyanum DC. (EL) has previously reported to exert anti-inflammation activity. Methods: In the present study, we examined the effects of the EL extract (ELE) on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD and potential molecular mechanisms. The anti-neuroinflammation effect of ELE was also determined in lipopolysaccharide (LPS)-induced BV-2 cells in vitro. Moreover, the ELE-interacting target proteins were identified. And the bioinformatics analysis was performed based on the identified targets. Results: Our results showed that ELE significantly alleviated motor performance impairment and neuronal damage in MPTP-induced PD mice. In particular, ELE reversed MPTP-induced neuroinflammation via inhibiting microglial activation that was associated with progressive PD. Moreover, the anti-neuroinflammation effect of ELE was confirmed in LPS-induced BV-2 cells by detecting the release of pro-inflammatory factors such as nitric oxide (NO), interleukin-6 (Il-6), tumor necrosis factor-α (TNF-α), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Furthermore, the ELE- interacting target proteins were identified by affinity purification-mass spectrometry-based proteomics strategy. Then, AMP-activated protein kinase (AMPK) signaling pathway was enriched by kyoto encyclopedia of genes and genomes (KEGG) analysis. We found that ELE markedly increased AMPK phosphorylation and inhibited nuclear factor-κB (NF-κB) signal in BV-2 cells. Conclusion: Collectively, these results indicate that ELE may exert significant neuroprotective effects against PD via targeting neuroinflammation.