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 alkanthiol self-assembled monolayers (SAMs) on Au(111) surface. The internal patterns in the simulated STM images are dependent on bias voltage and alkanethiol chain length, and have characteristic of the topographic effect modulated by the electronic effect. The electronic structure of the adsorption system is analyzed for discussing STM imaging mechanism of alkanethiol SAMs. Besides enhancing the intermixing between alkyl part and Au substrate states, sulfur atom in alkanethiol obviously influences the pattern in STM image by its chemisorption mode on Au(111) surface. Simulated images qualitatively reproduce STM experimental results.