Micro-lens array (MLA) has been widely used for 3D imaging etc., due to its excellent functional performances. Ultra-precision diamond turning (UPDT) offers a satisfying solution to the fabrication of micro-lens array with sub-micron form accuracy and nanometric surface roughness. However, the deviation between spindle to tool tip, i.e. tool setting error, is a crucial factor deteriorating form accuracy in UPDT. This study focuses on discussing the effect of tool setting errors on form error in UPDT of MLA. Firstly, a theoretical model was established to analyze the form error of MLA induced by tool setting.Moreover, a new two-step tool setting method was employed for reducing or eliminating the tool setting errors. Finally, experiments were carried out considering the tool setting effect in UPDT of MLA. The results indicated that the proposed tool setting method can achieve a high-precision accuracy and the distribution of form error obtained from experiments was in a good agreement with theoretical model.Signi cantly, the study draws up an understanding of the tool setting effect on form accuracy in UPDT of MLA with the further improvement.