The activation of melatonin receptors, belonging to the G-protein coupled receptors (GPCRs) superfamily, has been recognized as a vital approach in the clinical management of sleep disorders. Although the natural agonist melatonin and synthetic agonists (e.g., ramelteon) targeting these receptors have been extensively studied, the identification of natural compounds acting as ligands remains elusive. We applied a combination of methods including GPCR-induced ERK1/2 MAP kinase phosphorylation assay, inhibition of forskolin-stimulated cAMP production, drug affinity responsive target stability (DARTS), cellular thermal shift assay (CETSA), solvent-induced protein precipitation (SIP), 2-[125I]-iodomelatonin binding assay, fluorescence resonance energy transfer (FRET), and molecular docking to investigate MT1 activation by gastrodin and the gastrodin–MT1 interaction. The in vivo study was performed with mice whose MT1 receptors were knocked down in the suprachiasmatic nucleus (SCN) of the brain. The sleep behavior and sleep-related hypothalamic neurotransmitters were evaluated. The results identified that the gastrodin acted as an agonist of MT1 through direct binding to the receptor. The interaction of gastrodin-MT1 was similar to that of melatonin–MT1. The in vivo sleep-promoting effect of the gastrodin depended on the presence of MT1 in the SCN and was associated with the hypothalamic neurotransmitters, similarly to melatonin.