Self-assembled monolayers (SAMs) of N-isobutyryl-L-(D)-cysteine (NI BC) on Au(111) surfaces were successfully prepared by immersing the Au(11) surfaces in the preheated pure NI BC aqueous solutions for a certain time and characterized by means of scanning tunneling microscopy. Close-packed lamellar structures with a rectangular (4 x root 3) lattice were found both in the SAMs of L-NIBC and D-NIBC. The pH value of the aqueous solutions was found to be sensitive to adjust the SAM structures during the assembly. Changing the pH value from 5 to 7 may completely shift the SAM structures from close-packed lamellar phase to loose-packed perpendicular phase. Combined with density functional theory calculations, such kind of phase transition was explained by the breaking of hydrogen bonds between carboxylic groups and the formation of extra interactions between COO- and Au.