Aerodynamic resistance changes in the atmospheric surface layers (ASLs), such as coastal zones and rural-urban interface, complicate the transport processes. Their effect on ASL flows is investigated by the large-eddy simulation (LES) with the one-equation subgrid-scale model. The roughness elements at the bottom are explicitly resolved by sinusoidal wavy surfaces to examine the coupling between roughness sublayers (RSLs) and inertial sublayers (ISLs). In view of the increasing (decreasing) aerodynamics resistance after an abrupt surface transition, the flows decelerate (accelerate) and the momentum flux increases (decreases). The adjustments initiate at the RSLs during the development of the internal boundary layer (IBL) so the flows hardly establish self-similarity immediately after surface transitions. The evolving IBL illustrates the flow adaptation to the downstream (new) surface. Unlike those analytical solutions, the current LES unveils a slower IBL growth in the streamwise direction, demonstrating the importance of resolving RSLs explicitly. Besides, augmented turbulent diffusion is observed over the rougher surface. The gradual adjustment of higher-order moments along with developing IBL confirms that IBL is a physically significant length scale. The spatial behaviours of skewness and kurtosis, which suggest coherent events, are visualized across the surface discontinuity. The wall-normal distributions of energy spectra show that the energy-carrying turbulence shifts to higher frequency over the rougher surface. Small-scale turbulence motions are adjusted in ISL. Moreover, the shift is completed substantially on large-scale RSL turbulence, demonstrating the significance of RSLs.