Fabrication of micro lens arrays has been a research hotspot in the area of micro optics. By using two X-ray moving lithography, the polymethyl methacrylate(PMMA) as the positive photoresist, the micro lens array was manufactured on PMMA plate, and its fabrication principle was described in detail. The related mask pattern for fabricating micro lens arrays was designed. Through designed mask patterns simulation, the shape of the actual micro lens could be predicted. After the first moving X-ray lithography, theoretically the semi-circular columnar micro 3D structure was formed on the PMMA substrate. If the mask mounted vertically was rotated 90° after the first X-ray lithography and the second X-ray lithography was carried out, eventually the 30×30 micro lens array was obtained on the 10 mm×10 mm PMMA substrate, the diameter of each micro lens was about 248 μm, the depth was about 82 μm. The relationships between the amount of X light exposure and the depth of PMMA etching was studied. The micro lens array profile measurement shows that the new method for the fabrication of micro lens array is proved to be feasible.