The groundwork of the security analysis theory of the network system is the systematic self-organization doctrine. For any network systems, whether it has entered the optimum category or gone out of non-optimum category are judged through self-organization theory. Because a network has to go through three attributes: dynamic, uncertainty and invented, it is characterized by the alternating occurrence of trust, non-optimum, optimum, and so on. In order to hold the network security in the optimum category under certain degree and stage, we have to recognize and control the non-optimum factors of the network through self-organization function. As we know, the self-organization system is not only dynamic, but also evaluative. In order to measure the degree of the evolution of the system’s self-organization, the criteria of evolution have to be set up (self-organization criteria). Different schools have different choice of the criteria and different opinions have to be applied in different systems. Generally speaking, from the viewpoint of the inner structural organization of the network system, network entropy (NE) and relevant parameters can be used as criteria, e.g. entity of the NE, upper-entity of the NE, and negative NE. As is explained in the statistics of entropies, the value of the network entropy proves how much chaos there are in the network system and when the network system achieves the thermodynamic balance, the entropy reaches maximum. Therefore, the direction, where the entropy decreases is called, as the direction where the network security optimization. That is to say the decrease of the entropy, the difference of the entropy and the maximum entropy can be taken as the measurement of the organization (the measurement of the trust network). From the viewpoint of the relationship of the network and the outside, there exist criteria of capacity and function. For example, the order references of the network system can represent the organization within the network as well as the relationship between the network and its outside. Therefore, the order reference can be used as a characteristic reference of the evolution of the self-organizing system. Except for the above two criteria of the basic self-organization, different self-organization criteria can be chosen depending on the different natures of network action systems