Chemerin, derived from tazarotenib-induced gene 2 (TIG2), is an endogenous ligand for the orphan G protein-coupled receptor chemokine-like receptor 1 (CMKLR1). Chemerin/CMKLR1 signaling system plays an important role in multiple tissues and organs, and there are multiple chemerin isoforms in vivo due to the C-terminal proteolysis by several proteases. This paper predicted and modeled the structure of six isoforms of chemerin by Alphafold2, and modeled three active isoforms in complex with CMKLR1, to elucidate the different binding sites of different isoforms. Additionally, the known small molecule antagonist of CMKLR1, 2-(α-naphthoyl) ethyltrimethylammonium iodide (α-NETA), was also modeled to dock with CMKLR1, and the binding sites of α-NETA with CMKLR1 were analyzed. From the protein molecular structure level, our results provide: (1) The mode of interaction between active chemerin and CMKLR1；(2) The mode of interaction between α-NETA and CMKLR1. This study provides theoretical basis and experimental basis for the design of targeted drugs for CMKLR1.