The importance of the cost issue in aviation market is growing day by day. Thus, the cost is analyzed adopting the system engineering analysis methods due to its complexity. Different needs from different stakeholders are captured to form the functional model and decomposition tree of civil aircraft cost. In addition, the specific analysis of the sub-function “decrease the Direct Operation Cost (DOC)” is carried out. The DOC design requirements in aircraft level are obtained and divided into system level. Design, verification and optimization processes and methods are derived for two concrete requirements, “decrease fuel cost” and “decrease direct maintenance cost”. The study would provide useful reference for the research of civil aircraft cost issue.