A low temperature scanning tunneling microscope (STM) has been employed to investigate the insulating alkanethiol self-assembled monolayers chemisorbed on Au (111) substrates. The STM images show clear intramolecular patterns, which are voltage-and site-dependent. Theoretical simulations, using the density functional theory, reproduce the experimental STM images. Our results show that due to the chemisorption, there are new states appeared in the energy gap of the alkanethiol, and they are mainly composed of Au and Sorbitals, mixed with a small amount of orbitals at the alkyl part. The STM only images the states localized at the tail carbon-hydrogen groups since the Au and S atoms are located farther from the STM tip, and the images can reflect the surface topography of such standing molecular layers.