A multiscale finite element method is applied to the Spalart-Allmaras turbulence model based detached-eddy simulation (DES). The multiscale method arises from a decomposition of the scalar field into coarse (resolved) and fine (unresolved) scales. It corrects the lack of stability of the standard Galerkin formulation by modeling the unresolved scales that cannot be captured by a given spatial discretization. The stabilization terms appear naturally and the resulting formulation provides effective stabilization in turbulent computations, where reaction-dominated effects strongly influence the boundary layer prediction. The validation of the multiscale-based DES is carried out on a backward-facing step. The time-averaged skin friction coefficient and pressure coefficient distributions are compared with the experimental and direct numerical simulation (DNS) results. Furthermore, the potential use of multiscale DES in computational wind engineering (CWE) is investigated. High-Reynolds flow over the Commonwealth Advisory Aeronautical Council (CAARC) standard tall building model is simulated by DES with both uniform and turbulent inflow. Time-averaged pressure coefficients on the exterior walls are compared with experiments. It is demonstrated that DES is able to resolve the turbulent features of the flow and accurately predict the surface pressure distributions under atmospheric boundary layer flows.