Surface roughness, compared with tiny sizes of micro products, can be relatively large and has significant influences on micro forming processes and products’ quality. In this study, a voronoi finite element model that considers size effects of material was developed. Next the surface roughness information was assigned to this voronoi model through different elemental thickness distributions. Furthermore, springback simulation was conducted for the micro deep drawn circular cups. Simulation results demonstrate that the surface roughness with consideration of size effects has significant influences on the overall springback, the drawability represented by the minimum thickness and products’ quality regarding thickness evenness and shape accuracy. This study also shows that the results from the new models are close to the experimental results concerning the diameter of cup mouth and the maximum drawing force. The developed model for the micro deep drawing is accurate and beneficial for the development of micro deep drawing process.