We investigated an annealing effect of self-assembled monolayers (SAMs) generated from derivatives of terphenylmethanethiols and tetradecanethiol (C14) on Au(111) using scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, and contact angle measurement. STM data revealed that the molecules were partially desorbed by the annealing process at temperatures where the contact angle of the hexadecane began to decrease. The decreases in contact angles of both the CF3- and CH3-terminated terphenyl SAMs were caused by annealing at 180 degreesC for 1 h, while a similar decrease began at a lower temperature of 150 degreesC in the C14 SAMs. From the STM data, a large amount of CH3-terminated terphenyl molecules remained after annealing at 180 degreesC for 3 h, while a small amount of molecules were observed in the other two SAMs. These data demonstrate that the CH3-terphenyl-derivatized thiol SAM had the highest thermal stability of the three SAMs, and the molecular backbone structure and end group were crucial for determining the thermal stability of the SAMs.