Abstract: The policy document reflects policy target and logic. The central government documents which are focused on reform of scientific research institution from 1984 to 2015 are used as the sample data and the reform process is divided into four stages. By using the institution change theory of D.C.North, the reform logic and difference among several stages are analyzed on the base of policy subject, cooperation network and policy theme. The Study shows that the reform is dominated by economic rationality, coordinated by the state council, pushed by the administrative system which is fragmented and there exists obstacle in different public sectors' cooperation. During the period of 1984-2002, the policy documents were designed to achieve the organizational reconstruction of scientific research institutes. After that, the property right system which is much accounted of is intended to be improved. However, the reform gets into stagnant because of the backward administrative system. Moreover, it’s no doubt that the reform of scientific research institution should be consistent with the marketization of economic system and related policy suggestions are put forward.