G-protein-coupled receptor 120 (GPR120), which functions as a new receptor for long chain free fatty acids, may play a role as a potential therapeutic target for type 2 diabetes mellitus. The three-dimensional (3D) structure of GPR120 is experimentally unavailable to date, however, leading to difficulty in the structure-based drug design. Based on the X-ray crystal structure of β2 adrenergic receptor, a homology model of the GPR120 was constructed, then, molecular-dynamics (MD) simulations were carried out for the entire system. The GPR120 ligand agonist GW9508 was docked into the optimized model, and the critical amino acid residues for binding were identified, which was very important for further site-directed mutagenesis study. The constructed models should provide a good starting point for further characterization of the binding models for GPR120 ligands. Furthermore, the method developed herein will be applicable to build other GPCRs.