Secondary metabolism plays an important role in plant life as well as the interaction between plants and environmental factors. Many secondary metabolites derived from plants have been used for the production of medicines, dyes, insecticides, food flavors, fragrances and so on. With increasingly comprehensive understanding of the plant metabolic networks, great progress has been made in the genetic improvement of plant secondary metabolic pathways through gene engineering. Strategies for the genetic engineering of plant secondary metabolism include: (1) enabling the host plant to accumulate a novel desirable compound by transformation of single/multiple enzyme gene (s) or a whole metabolic pathway; (2) decreasing target gene expression or inhibiting competitive metabolic pathway to achieve metabolic flux towards higher production of particular molecules through antisense RNA and RNA interference technologies; (3) effectively manipulating the transcription factors responsible for the metabolic regulation at multiple steps in a given pathway so as to have a great synthesis of the target bio-chemicals. Basing on author's research work on flavonoid synthesis mechanism in soybean seed and its gene engineering, recent progress in the engineering of plant secondary metabolism involved in the synthesis of anthocyanins, flavonoids, alkaloids, terpenoids, benzoic acid derivatives etc are reviewed.