The dissimilarity of dynamics and turbulence structures between the roughness and inertial sublayers (RSL, ISL) over roughness elements show that ISL turbulence is much more homogeneous. Conventional logarithmic law of the wall is merely applicable for the RSL mean-wind-speed profiles. To characterize the turbulence scales and elucidate the mechanism, the flows in the atmospheric surface layer (ASL) over real urban morphology are measured in wind tunnel experiments fabricated by 3D-printing, reduced-scale model of downtown Kowloon Peninsula, Hong Kong. Elevated dispersive stress at urban canopy signifies the influence from individual buildings and inhomogeneous RSL flows. A positive momentum contribution appears in the low-frequency regime. The large-scale turbulence in RSL thus enhances the mixing and transport, resulting in inhomogeneous flows. The contribution from ejection Q2 and sweep Q4 increases and decreases, respectively, with increasing RSL motion strength. The conventional −5/3 law is observed by empirical mode decomposition (EMD) and the largest amplitude fluctuation occurs more often when the turbulence length scale is comparable to the turbulent boundary layer (TBL) thickness. The single-point amplitude modulation (AM) shows that the large- and small-scale turbulence correlates tightly at the bottom of RSL. Besides, the joint probability density function (JPDF) illustrates that accelerating large scales often occur with decelerating small scales, and they are intensified with increasing wall-normal distance. As a result, large-scale turbulence influences substantially the flow structures over urban areas and the small-scale turbulence (even) in RSLs in the vicinity of building obstacles.