Micro deep drawing is a promising manufacturing method to produce the hollow, thin walled, cup or box like products at micro scale. Forming velocity can affect the products’ quality significantly due to the size effect, and this effect can be various with different thickness material. In this study, 30, 40, and 50 µm thickness stainless steels were annealed at 950 °C for 2 min under protection of argon gas ambient respectively. These different thickness steels were utilized in the micro deep drawing with different forming velocities. The experimental results show that, the profile accuracy and surface quality of the micro product are affected by changing the forming velocity with different thickness blanks. The micro cup has a less indentation area at the bottom and becomes rounder and more symmetrical with a thicker blank. Besides, the wrinkling phenomenon turns distinct with a thinner blank, and the earing becomes more significantly when increasing the drawing velocity or decreasing the blank thickness. When the drawing velocity or blank thickness increases, the surface of the micro cup becomes smooth and even. The experimental results are in good agreement with the simulation results, which confirms the developed finite element simulation model is applicable.