From the historical perspective, this paper attempts to use the analytical framework of “risk control-governance performance” to explain the institutional motivation of the change of social organizations system. According to the research, the government’s system design is the periodic adjustment between“constraint” and “incentive”, and the institutional logic is governance performance based on controllable risks. The policy orientation of the central government and local governments on social organizations are different, and on the whole, it is manifested as macro risk-aversion and medium empowerment. The state’s absorption and empowerment can coexist, so the other side of absorption is exclusion and alienation. While social organizations’ governances are entering the new stage of “order thought replacing stability thought”, local governments should pay more attention to the differentiated ecology about them.