Large-eddy simulations (LES) are performed to simulate the flow and scalar transport in rural-to-urban transition regions. The LES framework is first validated with wind-tunnel experimental data of scalar dispersion within and above a staggered array of cubes. It is then used to simulate the scalar dispersion in transition regions from a flat homogeneous terrain to uniform arrays of cubes with height h. Staggered cube arrays with five different plan area densities, equal to 0.028, 0.063, 0.111, 0.174 and 0.250, and two incoming wind directions (α), equal to 0° and 27° are considered. Above the cube array, self-similar profiles for the mean scalar concentration are found and a scalar internal boundary layer is identified in all the cases. For all the cases tested, larger internal boundary layer thickness is found for α = 27° compared with that of α = 0°, which is related to the higher effective surface roughness in the cases of α = 27°. Within the urban canopies, the scalar concentration is found to adjust quickly within the cube array, which leads to a similar scalar concentration distribution pattern after the second row of cubes. Comparing the cases of the two different α , similar scalar concentration and adjustment pattern are found when the density is low. However, when the density is higher, higher scalar concentration is found in the cases of α=27∘ compared with those of α=0∘.