This paper proposes the systematic design approach for developing the evaluation indicators that evaluate the candidate proposals in the national defense core-technology R&D projects. To improve the validity and fairness of the evaluation indicators, the existing evaluation process in a military and a public sector are surveyed and also the existing evaluation system of the core-technology R&D programs for the national defense is analysed and discussed. A new system for the evaluation indicators is designed by using the axiomatic design, factor analysis and the analytic hierarchy process. It is expected that the proposed evaluation indicators contribute to enhance the fairness and the reliability of the evaluation process for the proposal of the national defense core-technology R&D projects.