GLP-1 receptor, one of the most successful targets for therapeutic drug development against type 2 diabetes and obesity, is known to engage multiple intracellular proteins to initiate different signaling pathways. However, due to technical challenges, it remains much less explored how the receptor interaction with proteins on the cell membrane mediates its signaling activity and physiological effects. Here, we present a ligand-based proximity labeling approach to be integrated with quantitative proteomics so as to interrogate the native cell membrane interactome for the GLP-1 receptor upon agonist simulation. With this approach, our study identified a number of unreported cell membrane interactors for the endogenous receptor in both a pancreatic β cell line and a neuronal cell line, which revealed interaction landscapes distinct from those previously mapped in less physiological cellular systems. We further demonstrate this strategy can be exploited to uncover new regulators of GLP-1 receptor-mediated signaling and insulinotropic response in β cells. Additionally, we obtain a time-resolved cell membrane interactome map for the receptor in β cells. Therefore, our study provides a new approach that is generalizable to map endogenous cell membrane interactomes for GPCRs so as to decipher the molecular basis of their cell-type-specific functional regulation.