<p>Subsurface plays a crucial role in determining the mechanical properties and reliability of materials in ultra-precision machining. This study proposes a multiscale crystal plasticity finite element (CPFE) model with the consideration of microscale and nanoscale size of precipitates in 6000 series aluminum alloys to study subsurface generation, the microstructure evaluation as well as the macroscopic mechanical behavior of aluminum alloy in ultra-precision fly cutting (UPFC). Experiments are conducted to study the milling parameters on subsurface damage characteristics of Al6061-T6 and RSA6061 under different milling conditions, including dislocation distribution and microstructure variation of aluminum alloy. The effects of grain size, precipitate size, cutting speed and depth of cut on the subsurface features including the subsurface microstructure variation, distributions of Mises stress and cumulative shear strain as well as the strain gradient of subsurface are qualitatively and quantitatively evaluated by the established CPFE model. The simulations and experimental results show that the subsurface of aluminum alloy lacks distinct fine-grained and transition layers, while the matrix layer exhibits a large number of annular grain boundaries. This study provides a new perspective for exploring the influence of precipitates on the plastic deformation behavior of the matrix.</p>