A method for preparing microlens arrays based on projection lithography was proposed, and microlens arrays of various calibers and different surface roughness were successfully prepared by the method. The method employs a 0.2× projection objective lens to reduce the manufacturing cost of masks and realize the preparation of microlens arrays with different calibers. We achieve superior surface figure accuracy while reducing the complexity of mask preparation by employing a projection-based mask-shift filtering technique. Four kinds of microlens arrays with different calibers, 50 μm, 100 μm, 300 μm and 500 μm, were prepared. The machining accuracy of the surface morphology reaches the sub-micron level and the surface roughness reaches the nanometer level. The experimental results show that this method has great potential in the fabrication of microlens arrays, and can achieve lower line width and higher surface profile accuracy than traditional methods.