The advanced manufacturing industry is located at the top of the manufacturing value chain. Its development is restricted by supply chain collaboration (SCC), the level of which is affected by many factors. Few studies comprehensively summarize what influences SCC and distinguish the impact level of each factor. Practitioners have difficulty isolating the primary factors that affect SCC and managing them effectively. Therefore, based on synergetics and the theory of comparative advantage, this study analyzes what influences SCC in the advanced manufacturing industry and how these influencing factors work, using data from 94 manufacturing enterprises and the Haken model to identify the influencing factors. The results show that China’s advanced manufacturing supply chain underwent a phase change and entered a new stage during 2017–2018. In the new stage, the competitive advantages of enterprises are one order parameter (slow variable) and are primary factors affecting SCC. The interest demands of enterprises are a fast variable and are secondary factors affecting SCC. The competitive advantages of enterprises dominate the interests of enterprises in affecting the collaboration level of China’s advanced manufacturing supply chain. In addition, in the process of influencing SCC, there is a positive correlation between the competitive advantages of enterprises and the interest demands of enterprises, and the two factors have a positive feedback mechanism. Finally, when the enterprises in the supply chain cooperate based on their differential advantages, the collaboration capability of the supply chain is at the highest level, and the overall operation of the supply chain is orderly. In terms of theoretical contribution, this study is the first to propose a collaborative motivation framework that conforms to the characteristics of sequential parameters, which provides a theoretical reference for subsequent studies on SCC. In addition, the theory of comparative advantage and synergetics are linked for the first time in this study, and both of them are enriched and developed. Equally importantly, this study compares the bidirectional influence between firms’ competitive advantages and firms’ interest demands and the ability of both to influence SCC, enriching previous validation studies of unidirectional influence. In terms of practical implications, this study guides top managers to focus on the management practice of collaborative innovation in the supply chain and advises purchasing managers and sales managers on selecting supply chain partnerships.