The adsorption and self-assembly structures of melamine molecules on an Ag(111) surface are studied by low temperature scanning tunneling microscopy (STM) combined with tip-enhanced Raman spectroscopy (TERS). Two ordered self-assembly phases of melamine molecules on Ag(111) were studied by STM and TERS, combining with first-principles simulations. The α-phase consists of flat-lying melamine molecules, while the β-phase consists of mixed up-standing/tilted melamine molecules. Moreover, dehydrogenation of melamine can be controlled by annealing the sample as well as by a tip-enhanced photo-catalytic effect. Our work demonstrates TERS as a powerful tool not only for investigating the configuration and vibration properties of molecules on a metal surface with high spatial resolution but also for manipulating the chemical reactions with tip and photo-induced effects.