When a shock wave releases from a metal-vacuum interface, some high velocity metal particles will be ejected from the metal surface which generally produce some tiny grooves on the metal surface. This phenomenon is often called the “micro-ejecta”. In this paper, we numerically investigate the effect of the micro-structures of these tiny grooves on the property of the micro-ejecta. To verify the numerical simulation model, a strict Pb micro-ejecta experiment is carried out, where the breakout pressure is about 40 GPa and the Pb target surface roughness is Ra1.6. The dynamic processes of the micro-ejection caused by the real surface groove of experimental target and simplified isosceles groove (both have a depth of 5 μm and wavelength of 75 μm), are respectively simulated by a two-dimensional smooth particle hydrodynamics method, and the effects of surface groove micro-structure on the micro-ejecta properties are examined. The simulation results of the tip velocity and accumulated mass, obtained from the real surface groove model, are in good agreement with the corresponding experimental results measured via DISAR and Asay foil, implying that the numerical result is exact. The tip velocity and accumulated mass caused by the real surface groove are much larger than those caused by the simplified isosceles groove, and a second ejection phenomenon is found in the micro-ejecta process from the real surface groove model. The process can produce some faster ejecta than a single ejecta process and influence the density distribution of the micro-ejection. It indicates that the micro-ejecta process can also be affected by the micro-structure of the metal surface groove, besides perturbation wavelength and surface groove depth.