The fly-cutting technique has wide application in optical microstructure manufacture. A unique method is put forward to achieve fast and high quality optical waveguide microstructure mould manufacture with fly-cutting technique after an analysis of the present complicated process technique. Fly-cutting orthogonal test was conducted to get the optimal process parameters for machining the waveguide mould. It is found that the microstructure surface roughness is sensitive to the cut depth first, the next two are the spindle speed and the feed speed. The optimal process parameters involve such figures as cut depth of 25μm, feed speed of 20mm/min and spindle speed of 800r/min through the experiment analysis considering the stability of the fly-cutting system and machining efficiency. The optical waveguide mold with microstructure surface root-mean-square roughness of 17.1nm was obtained through the optimal process parameters.