The fabrication of optical elements with microstructural arrays has attracted more and more attention. Single-point diamond flying cutting technology has been gradually applied to the fabrication of microstructures with the advantages of high efficiency, low cost and high machining accuracy. This paper mainly studies the influence of repeated positioning errors of machine tools and errors introduced by cyclic machining on micro-structure turning effect when flying cutter turning micro-pyramid structure, analyses the conditions of secondary groove generation in V-groove turning, studies the methods of restraining secondary groove generation, and finally verifies through expe-riments that the generation of secondary groove can be restrained by controlling the turning depth greater than the minimum turning depth.