A variational multiscale (VMS) formulation of the compressible Navier–Stokes equations is investigated for the simulation of weakly compressible flows. The method employs a residual-based scale separation in which numerical stabilization is confined to the unresolved scales, allowing the resolved flow structures to remain minimally dissipative. This formulation is particularly suited for strongly nonlinear dynamics where conventional stabilization strategies may compromise accuracy. The approach is evaluated on canonical benchmark problems, including the Taylor–Green vortex, Rayleigh–Taylor instability, and Kelvin–Helmholtz instability, which are characterized by broadband scale interactions and rapid instability growth. An adaptive octree-based mesh refinement framework is used to dynamically concentrate resolution in regions of high gradients and evolving small-scale features, enabling efficient control of computational cost. The results demonstrate that the proposed VMS formulation provides a robust and accurate framework for capturing multiscale flow physics in weakly compressible regimes, consistent with the principles of scale-selective stabilization and efficient high-fidelity simulation.