One application of the lattice Boltzmann equation (LBE) models is in combination with tomography to simulate pore-scale flow and transport processes in porous media. Most LBE models in the literature are based on cubic lattice, and if the voxels in a tomography image are not cubic or cannot be divided into cubes due to computational limitations, these models will lose most of their advantages. How to deal with such images is, hence, an interest in use of the LBE model to simulate pore-scale processes. In this paper, we present an orthorhombic LBE model based on the single-relaxation time approach with the relaxation parameter varying with lattice directions. The equilibrium distribution functions in the standard LBE model were modified to correct the anisotropy induced by the non-cubic lattice, and the calculations of the fluid density and momentum were also redefined in order to maintain the conservation of mass and momentum during the collision. We tested the model against analytical solution for fluid flow in a tube, and against the standard cubic-based LBE model for fluid flow in a duct with an island inside. The model was then applied to simulate fluid flow in a 3D image in attempts to analyse the errors if the voxels in the image are not cubic but are assumed to be cubic.