Development of the system that has required performance is the most important figure and that is the key of project succeed. In order to perform that, systems engineering has come to the fore as a solution. In each step of system engineering process, particularly, requirement analysis and derivation, logical solution, architecture design step are known to affect many of the function and efficiency. Of these, this paper focus on architecture design. We introduce methodology for physical architecture design by applying DSM(Design Structure Matrix) methodology which is based on result of logical solution from MBSE methodology.