On the basis of investigations on the evaluation of the scientific and technological innovation capacity, such hot topics as national defense research institutes and the essence of their scientific and technological innovation capacity are discussed. Around one of constructive elements of the scientific and technological innovation capacity, “One Divides into Two”, a new strategy is introduced with the case study of China Academy of Engineering Physics, namely the scientific and technological innovation capacity can be evaluated from both common competence and core competence. To achieve the purpose of “grasp the core competence, emphasize the promotion of the overall scientific and technological innovation capacity of the national defense research institutes”, the evaluation method of “two-system and three-stage” is presented. The new strategy and the evaluation method can be helpful to the evaluation of the scientific and technological innovation capacity of the national defense research institutes.