In one embodiment, a topography simulation apparatus includes a division module configured to divide topography of a substance of a semiconductor device into first to n-th layers, where n is an integer of two or more. The apparatus further includes a flux calculation module configured to calculate, for each of the first to n-th layers, a flux of particles which reach a surface of the substance in each layer. The apparatus further includes a topography calculation module configured to calculate, for each of the first to n-th layers, an amount of change of the topography of the substance in each layer based on the flux.