TGR5, a G-protein coupled receptor, acts as a promising target for the treatment of diabetes, obesity and metabolic syndromes. Understanding the activation of TGR5, the structural conformation and the mode of mechanism upon binding with agonists is crucial for the development of new drugs. In the absence of experimental data, homology modeling was performed to predict the structure of TGR5. Molecular dynamics simulation of 100 ns was performed to investigate the stability of the constructed model embedded in a lipid bilayer. A combined method consisting of molecular docking and binding free energy calculations was performed to understand the binding mechanism of two experimentally proved selective TGR5 agonists. Additionally, 30 ns of protein–ligand complex dynamics were performed to reproduce the mechanism of interaction. Both agonists shared a similar binding mode and showed four common hydrogen bonding interactions with TGR5. Thus, the results could provide more knowledge on the activation of TGR5 by agonists and prove helpful in the development of novel potent agonists.