The adequate interpretation of scanning tunneling microscopy (STM) images of the clean Si(001) surface is presented. We have performed both STM observations and ab initio simulations of STM images for buckled dimers on the clean Si(001) surface. By comparing experimental results with theoretical ones, it is revealed that STM images depend on the sample bias and the tip-sample separation. This enables us to elucidate the relationship between the corrugation in STM images and the atomic structure of buckled dimers. Moreover, to elucidate these changes, we analyze details of the spatial distributions of the π, π * surface states and σ, σ * Si-Si bond states in the local density of states which contribute to STM images.