The free energy gradient method was applied to the multidimensional geometry optimization of glycine zwitterion (ZW) in aqueous solution in order not only to demonstrate its applicability, but also to examine its efficiency. The method utilizes force on the free energy surface that can be directly calculated by the molecular dynamics method and the free energy perturbation theory. Then, the most stable ZW structure in aqueous solution was obtained within the tolerance assumed, and it was found that the free energy (FE) and enthalpy changes of stabilization from the initial geometry optimized in the gas phase are -0.9 and -3.5 kcal/mol, respectively, and the amino and carboxyl groups are spatially separated by each other due to their solvating with water molecules. Comparing the contributions of enthalpy and entropy to FE, the former is attributed to the main origin of FE stabilization during the optimization procedure, and it was found that solvation entropy prevents water molecules from solvating the ZW more strongly.