Flavonoids are the major secondary plant metabolites with antioxidant activity. Because of its relative abundance in edibles including vegetables, especially onions, fruits, tea and wine [1], Morin and Quercetin are among the flavonoids attracting most attention. It has been reported to have biological properties that may play an important role in the prevention of human diseases, such as cancer, cardiovascular diseases, diabetes, ulcer, cataract and allergies [2]. Optimizing the effective factors was done in two stages. First, the effective factors were identified by PBD(Plackett Burman Design), then the meaningful factors were optimized by CCD(Central Composite Design) and the optimized conditions for AALLME were used for the analysis of Morin and Quercetin.