The microstructures on flexible membrane substrate prepared by the traditional methods may introduce large morphology and position errors, making it hard to achieve clear imaging. In this paper, we present a high precision fabrication method composed of two steps: unstressed fixation of the polyimide membrane and high precision fabrication of diffractive microstructures on the flexible membrane substrate. By using precise spin-coating technology, we get 25 μm thick polyimide membranes, whose coefficient of thermal expansion is almost zero. To prepare high precision microstructures, we propose an aerated membrane method, by which the flexible membrane substrate and the photoresist on it can attach tightly to the mask under the air pressure difference between the upper and lower surfaces of the membrane substrate during the contact lithography. The results show that the wave-front error obtained by this method is less than 1/30λ RMS (F# = 25@632.8 nm) at 400 mm aperture, indicating the microstructures have excellent morphologies and high position accuracy. © 2009-2012 IEEE.