The scientific nature of the structure of the system, the autonomy of the process of institutional construction and the effectiveness of the system operation are the three dimensional elements that have impact on the validity of the system. The system is a complex system, which consists of the system at the fundamental level, the system of the meso—level and the mechanism of the micro level. From the perspective of fundamental system, the socialist system with Chinese characteristics is distinctive and efficient, but it is not perfect and mature in terms of system and mechanism. This means that the firm confidence of the system does not signify that the shortcomings objectively existed in the institutional mechanism level can be ignored. In general, these shortcomings are embodied at three levels: the overall level of system and mechanism construction lag behind the needs of economic and social development. Too much attention is paid to quantity construction while quality improvement and execution effectiveness are neglected. In the process of system construction, overcoming shortcomings is a complex system engineering, which needs to grasp the key link. In this regard, the four basic projects should be emphasized: to promote the optimization of the system, to bring into play the positive effect, to enhance the executive force and to absorb the achievements of human civilization.