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Molecular dynamics simulations are carried out to investigate the deformation response during shock compression of nanocrystalline Al microstructures at the atomic scales. The shock response is investigated for various grain sizes (18 nm–100 nm) and impact velocities (700 m/s to 1500 m/s). The simulations suggest an increase in shock front width and a decay in the velocity and the amplitude of the elastic precursor wave (Hugoniot elastic limit) as the wave travels through the microstructure. For a limited sample depth of 500 nm of polycrystalline Al, the Hugoniot elastic limit (HEL) values are higher for larger grain sizes due to a lower density of grain boundaries and higher for higher piston velocities/shock pressures. Quasi-coarse-grained dynamics (QCGD) simulations are carried out to extend this investigation of the shock response of polycrystalline microstructures to the mesoscales. The capability of QCGD simulations to reproduce the atomic scale evolution of dislocation density fractions and shock wave structures is first demonstrated for a 100 nm grain-sized Al system. The evolution of shock front width, HEL, and dislocation densities are investigated for microstructures with grain sizes ranging from 100 nm to 800 nm and system lengths ranging from 600 nm to 9.6 μm. The MD and QCGD simulations indicate that the decay behavior is attributed to the capability of the shock wave to generate Shockley partial dislocations in the compressed microstructure. The simulations indicate that grain size and impact velocities affect the rates of generation of Shockley partials and hence affect the decay of the HEL. The MD and QCGD predicted values for HEL reported here show excellent agreement with the experimentally observed sample thickness dependence for Al. An empirical model is developed to predict the HEL of Al microstructures with grain size, shock pressure and sample depth as variables.