According to the coexist characters of technological, R&D and innovation, high profitability and the nature of State-owned of the state-owned enterprise of science and technology, this article constructs?a hierarchy performance evaluation index system?from?five aspects including?the financial, stakeholders, R&D and innovation, internal business processes and operations, learning and growth based on the?theory of the Balanced Scorecard. It includes three layers of target layer, criterion layer and index layer from the perspective of hierarchical structure of index system. It fills the gaps in research field of the performance evaluation system of the?state-owned scientific and technological enterprises?in a certain extent. By using the method of extension analytic hierarchy process, the weights of the performance evaluation system are calculated and the inaccuracy of the fuzzy subjective judgments and the inconsistency of the judgment matrix in the process of model construction are solved. Finally, the weights of the index system are calculated by the judgment of the evaluation index system investigated from the experts.