Modern industry has become very complex and requires an equally complex engineering technology system, which includes resource utilization, energy conversion, product research and development, technological innovation, environmental protection and industrial ecology, and other aspects of the system. Continued development of large-scale, streamlined, and continuous processes is critical; however, there are also problems such as data redundancy, overcapacity, redundant construction, and waste of resources. Based on the system synergy theory, this paper introduces the system analysis method from the perspective of flow structure, with the purpose of solving the management defects of complex industrial production systems. First, we analyze the complex industrial production system as a collaborative structure of three subsystems: material flow, energy flow, and information flow. The following concepts are clarified: “material flow is the main body, energy flow is attached to and drives material flow, material flow and energy flow generate information flow, and information flow reversely drives material flow and energy flow”. Secondly, the collaborative evolution process of the complex industrial production system is divided into three periods, which are the generation period, the stalemate period, and the maturity period, and a synergy degree evaluation model is established, which considers the Theil index and subsystem gray correlation method, and extends the dynamic differential equation model of three-stage collaborative evolution. Subsequently, we used MATLAB numerical simulation to demonstrate that the collaborative evolution of production systems is related to four aspects. They are the self-organizing ability of the system, the dominant role of order parameters, the competition and cooperation between order parameters, and whether mutations can become order parameters. At the same time, it was also found that it is basically independent of other factors, such as attenuation inertia. Then, the self-organizing map network (SOM) algorithm was used for the rapid identification of mutation data. Finally, we use the empirical research of SG enterprises to show that their production level and management system are advanced, but they were in a non-cooperative state from 2014 to 2021. In 2022, they had the basic conditions and trends to enter the synergistic generation period, and a synergistic management model is required. At the end of the article, we give a collaborative management method for complex industrial enterprises with a good management foundation. These include the management mechanism based on flow structure collaboration and the management path based on collaborative evolution. Of course, the management countermeasures given in this study are also applicable to other complex process-based industrial enterprises.