Functional conformational transition in the glutamine-binding protein (GlnBP) is known to be the key to bind and transfer ligand glutamine. Here, we developed a structure-based double-well model to investigate the thermodynamic and kinetic natures of the GlnBP conformational transition. We uncovered the underlying free-energy landscape of the conformational transition with different temperatures. The analysis shows that below the melting temperature, two basins of attractions emerge, corresponding to the open state and the closed state of the protein. We explored the kinetic property of the conformational switch through the mean and distribution of the first passage time as well as the autocorrelation function. The kinetics implies the complexity and the hierarchical structure of the underlying energy landscape. We built the contact maps of the structures to probe the structural evolution of the conformational transition. Finally, the φ values of the residues were calculated to identify the important residues (hot spots) of the transition state.