To solve the problems such as big alignment deviation， inconsistency between the entity and the digital model and high processing cost in the processing of the positioning pin hole on the melon petal male mold， the alignment method was improved. By combining coarse alignment and fine alignment， as well as using the 3D edge finder to perform the program verification， the goal of accurate alignment between the theoretical digital model and the entity was achieved. On this basis， through the coordinate transformation of the ellipsoid parameter equation， the processing of the normal and axial positioning pin holes on the ellipsoid surface on the 3-axis machine tool is accomplished. Consequently， with the help of the improved processing method， the hole position accuracy reaches Φ0.1 mm and the processing cost is reduced by 75%. This improved method should be promoted and utilized in engineering applications.