On the basis of Qian Xuesen’s systems thinking,a new discipline,the knowledge systems engineering,has been established.The mission and contents of this new discipline were introduced. Knowledge system is considered as “the system of systems” since most of the component systems is existing and they can be operated and managed independently. Integration of existing systems together with newly developed system will constitute the system of systems and new functions will emerge.The network models are widely used in knowledge systems and “system of systems” can be modeled and analyzed by the “network of networks” or so called supernetwork approach. The architectures of knowledge systems were suggested. They are (1)organizational architecture, (2)personnel architecture, (3)technological architecture, (4)business architecture, (5)cultural architecture. The working processes of knowledge system, including the knowledge acquisition, organizing, discovery, creation and utilization were analyzed. Some new concepts of knowledge conversion opposed to dichotomy approach, based on knowledge spectrum approach,were presented and integration of incremental and catastrophic evolution of knowledge creation model was suggested. The features and advantages of innovation by systemintegration and its thinking styles were described. Finally the architectural features of knowledge systems engineering in accordance with the framework of Qian’s taxonomy were discussed.