Based on the basic characteristics of core competitiveness of scientific research institutes, this paper analyzed the key factors affecting the core competitiveness of scientific research institutes, constructed the evaluation model of the core competitiveness of scientific research institutes from the perspective of strategic management, resource support capabilities, technology innovation, organizational management capabilities, and then used Entropy-Topsis evaluation model to evaluate 26 typical scientific research institutes’ core competitiveness, drew the construction level of the core competitiveness of scientific research institutes at this stage, cleared a path to enhance the core competitiveness, and provided a theoretical basis and practical guidance of scientific research institutes core competence evaluation and optimization construction.