Abstract: Fructose-1,6-diphosphate (FDP) is a naturally occurring allosteric effector which plays a direct role in important metabolic pathways other than glycolysis. In order to enhance the yield and producitivity of FDP, researchers have focused almost exclusively on enzyme amplification or other modifications of the pathway. Overproduction of FDP, however, requires significant redirection of flux distributions in the primary metabolic, but metabolic pathways of FDP have evolved to exhibit control architectures that resist flux alternations at branch points. This paper studies both under unperturbed condition and under several experimental perturbations at anaerobic glycolysis in Saccharomyces Cerevisiae whose cell permeability has been altered. The results showed that the branch points of glucose-6-phosphate (G6P), FDP and phosphoenolpyruvate (PEP) are principal nodes and the PEP node is a rigidity node. After the metabolic pathway is regulated by chemical regulative factor, node rigidity of PEP is alleviated and the flux of FDP accumulation out of the cell increases to 41.9 from 16.1, The conversion of FDP to glucose and phosphate increases from 14.3% and 41.2% to 41.1% and 92.7%, respectively.