The α-Synuclein (α-syn) and tau have synergistic effects on neurodegenerative diseases induced by environmental factors or genetic mutation. Thus, we investigated the role of α-syn and tau in neurodegeneration induced by chronic methamphetamine (METH) exposure (1.0∼20.0 mg/kg/d body weight, for 14 consecutive days). Here, we present a mice model with evidences of α-syn and tau participating in toxicology in chronic METH. METH increased α-syn level in the stratum oriens, pyramidal layer, stratum radiatum and stratum moleculare of hippocampal CA1, CA2 and CA3, polymorph layer of hippocampal dentate gyrus (DG), and substantia nigra (SN). The subcellular locations of the upregulated α-syn were mainly found in mitochondria and axons. The METH upregulated α-syn may directly induce mitochondrial damage, myelin sheath destruction, and synaptic failure. Also, the excess α-syn might indirectly promote tau phosphorylation through tau kinase GSK3β and CDK5, leading to microtubule depolymerization and eventually fusion deficit of autophagosome and lysosome. In the in vitro experiment, the autophagic vacuoles failed to fuse with the lysosome. The neuropathology induced by both the direct and indirect effects of α-syn could be alleviated by α-syn knockout. Taking together, these results indicate that the α-syn mediates the neurodegenerative process induced by chronic METH and that reducing α-syn might be a potential approach to protect the toxic effects of METH and also be, to a broader view, of therapeutic value in neurodegenerative diseases.