The shortcomings of the methods for system architecture design and evaluation are summarized.Analysis is made to data characteristics and information fusion requirement of sensors in avionic system, and a system design approach is proposed based on modified JDL model and data fusion tree.The operating mechanism of the system architecture based on a combat case shows that:the system architecture has the advantages of dynamic configuration and less calculation cost, and can satisfy the requirements of command and control system.System evaluation method is introduced to make qualitative and quantitative analysis to two typical system architectures, which shows that the evaluation scheme is scientific and effective.