We conducted large‐eddy simulations over 98 urban arrays with varying building densities and height distributions. Compared to uniform‐height urban arrays, the influence of height variability on urban flow is pronounced and acts differently in two idealized urban configurations: the low buildings induce higher wind speed and stronger turbulence over staggered arrays but act inversely over aligned building configurations. The flow motions around tall buildings generate strong dispersive fluxes, which are sometimes of similar magnitude to the turbulent momentum flux and responsible for a persistent isolated roughness flow pattern in the upper canopy regardless of the urban density. Tall buildings further contribute disproportionately to the form drag of the urban surface, reaching up to 3.9 times the form drag induced by buildings of height equal to the average building height, in dense layouts. The flow inflection points ‐ i.e., the largest wind speed gradient that defines the aerodynamic interface between the urban canopy flow and the surface layer flow above, are found to be displaced to the maximum building height if less than 25% of buildings are below the mean building height. These findings provide critical insight for the development of urban canopy models, where the impacts of height variability on flow are often linked to the vertical variation in urban density alone. To address this deficiency, we provide a case study that considers the drag amplification due to the impact of vertical urban structures in the urban canopy model, enabling high‐resolution regional climate models to reproduce urban air flows better.This article is protected by copyright. All rights reserved.