Parkinson's disease (PD) is a neurodegenerative disease characterized by dopaminergic neuron loss and Lewy bodies in the substantia nigra. Abnormal mitochondrial function and accumulated α-synuclein (α-syn) are key etiological factors of PD. Melatonin type 1 receptor (MT1) regulates sleep upon activation by melatonin and may be reduced in PD patients. However, the role of MT1 in PD pathogenesis remains elusive. In this study, we found knockdown of MT1 caused mitochondrial dysfunction, mitochondrial fission and mitophagy in SH-SY5Y cells. Expression of mitochondrial fission protein dynamin-related protein 1 (DRP1) was increased and expression of fusion proteins optic atrophy 1 (OPA1), mitofusin 1 (MFN1) and mitofusin 2 (MFN2) were decreased. This was probably attributed to decreased phosphorylation of DRP1 at S637 by protein kinase A (PKA) and increased phosphorylation at S616 by extracellular-regulated kinase 1/2 (ERK1/2). Loss of MT1 exacerbated mitochondrial fission without influencing mitophagy, TH expression and movement in an MPTP-induced mouse model. Neuronal MT1 deficiency aggravated preformed fibrils induced autophagy inhibition and α-syn aggregation. Overexpression of MT1 reduced mitochondrial fission, increased LC3II expression and decreased P62 accumulation to promote autophagy in HEK293T cells, thus mitigating aggregation of α-syn. This study demonstrates the function of MT1 in mitochondria and autophagy, which sheds further light on PD prevention targeting MT1.