The density functional theory calculations with local density approximation have been performed to simulate scanning tunneling microscopy (STM) images of individual molecules in close-packed upright alkanethiol self-assembled monolayers (SAMs) on a Au(111) surface. The internal patterns in the simulated STM images are dependent on bias voltage and alkanethiol chain length and have characteristics of the topographic effect modulated by the electronic effect. The electronic structure of the adsorption system is analyzed for discussing the STM imaging mechanism of alkanethiol SAMs. Besides enhancing the intermixing between the alkyl part and the Au substrate states, the sulfur atom in alkanethiol obviously influences the pattern in the STM image by its chemisorption mode on the Au(111) surface. Simulated images qualitatively reproduce STM experimental results.