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Abstract Neuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (Y₁R) in complex with G_i1protein. The NPY C-terminal segment forming the extended conformation binds deep into the Y₁R transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with Y₁R extracellular loops, contributing to the high affinity of NPY for Y₁R. The structural analysis of NPY-bound Y₁R and mutagenesis studies provide molecular insights into the activation mechanism of Y₁R upon NPY binding.