The effects of the secondary metabolite biosynthesison the metabolism and morphology of the Monascuspurpureus were investigated in this study. Hypha andseptum length became longer after deletion of genes pigRand pksCT in M. purpureus LQ-6 by Agrobacteriumtumefaciens-mediated transformation technology, highlybranched hyphae, much smaller and freely dispersedmycelial pellets were observed in M. purpureus. Comparedwith that in the wild-type, the level of intracellular NADHand NADPH was almost constant in M. purpureus DpigRat 4 days, but the NADH and NADPH levels decreased by1.58-fold and 3.71-fold in M. purpureus DpksCT. Thepresent study can not only provide a kind of strategy toimprove the Monascus pigments production, but also providetheoretical support for the further study of relationshipbetween the secondary metabolites, metabolism and morphologicalchange.