This paper discusses the differences of the emphasis of human-machine system design between complex information system and Internet products， how to transform functional requirements into design requirements， break through the traditional extensive design， and improve the human-machine coordination and human-machine interaction ability of air defense and anti-missile radar， and puts forward a effectiveness centered design idea and theory based on mission characteristics and timing sequence. This paper presents a new scientific design method for the key links affecting the combat effectiveness of human-machine system， such as human-machine function allocation， intelligent decision support， station division， information architecture of interactive interface and so on. The practice shows that the effectiveness centered design theory and method based on mission characteristics and timing sequence effectively improves the combat effectiveness of weapon equipment human-machine system. This method can effectively guide the human-machine system design of complex information system represented by air defense and anti-missile radar， and can be widely used for all kinds of human-machine systems with strong timeliness.