Abstract: Plant secondary metabolism is resulted from the interactions between plants and environment during the long-term evolution process,and is derived from the so-called primary metabolism.Terpenoids,alkaloids and phenylpropanoids are the three main types of plant secondary metabolites,whose metabolic pathways mostly exist in a way of metabolic channels,and the pathways possess the characteristics of species,genus and the phase of growth and development.The paper presents the discussions on the classification of plant secondary metabolites,the metabolic pathways and the gene engineering of metabolic regulations,in order to provide theoretical bases for comprehensively understanding the plant metabolism network,their reasonable positioning of secondary metabolism and its key enzymes,and for stimulating the sustainable exploration of wild plant resources.The discussions were emphasized on the biosynthetic pathways of the secondary metabolites and some other aspects including genetic improvement strategies on plant secondary metabolic pathways by gene-engineering technology.The paper also pays much more attention to expound the application perspectives of the functional genomic and metabolomic techniques to the studies on biosynthesis and regulation of plant secondary metabolites.