The nano-punching characteristics of single-crystalline aluminum are investigated using the quasi-continuum (QC) method. Four variables (i.e., crystal orientation, workpiece thickness, clearance between the punch and the substrate, and the taper angle of punch) are used to explore their effect during the nano-punching process. The shear stress distribution is used to express the punching effect on the punch and on both sides of the substrates. Besides, fracture strength, residual flash, and the atomic displacement vector are observed and discussed regarding the behaviors of the nano-punching process under various conditions. Based on the results, the Al workpiece with the X[111]Y[−110] orientation presents less lattice resistance during the punching process. Besides, the thickness of the workpiece has a significant effect on the punching quality. Workpieces with thickness values of 5 and 10 Å are more suitable for punching, due to stable loading and unloading stress–displacement curves and less residual flash on the cutting surfaces of these workpieces. In contrast, the effect of clearance has less impact on the punching behaviors of thinner workpieces. However, for thicker workpieces (i.e., 15 and 20 Å), a larger clearance will likely cause more residual flash. Furthermore, the taper angle of the punch should not be larger than 10°, otherwise, it might damage the workpiece and the substrate.