Water, as a ubiquitous and essential component of life, is known to have a significant impact on the structure and function of organic molecules. In this study, we investigate the role of water in the phase transition of organic molecular assembly structures by scanning tunneling microscopy at room temperature. The results show that the -O-H···O hydrogen induced by water molecules can lead to a significant structural transition in the molecular assembly, specifically through selective weakening of -C-H···O between 6-aminonicotinic acid and the formation of new -O-H···O bonds between 6-aminonicotinic acid and water molecules. Subsequent thermal treatment of these molecular assembly structures reveals that the formation of -N-H···O hydrogen bonds induced by water molecules has created a different pathway for the phase transition of the molecular assembly structure. This knowledge has important implications for the design of organic molecules with specific nanostructures that can be controlled through hydration.