In the era of technological innovation, the high-quality development of academic journals has placed urgent demands on the innovative thinking and capabilities of editors. This article introduces synergy theory and re-examines the cultivation of innovative thinking and capability among academic journal editors within this theoretical framework. The core concepts of synergy theory—open systems, self-organization, competition and cooperation, and the dominance of order parameters—exhibit profound structural similarities with the operational logic of the editorial department, and thus offer strong reference significance for how to stimulate the intrinsic innovative motivation of academic journal editors and how to design external cultivation mechanisms. Based on synergy theory, this article systematically analyzes the deep-seated reasons for the insufficiency of innovative thinking and capabilities among academic journal editors. Four causes are identified. First, there is a systemic ecological imbalance: insufficient external resource input and a lack of innovation vitality; second, the conditions for self-organization are absent: the individual innovation initiative of editors is weak, and innovation is difficult to spontaneously emerge; third, the competition and cooperation mechanisms are absent: the fundamental driving force for innovation is insufficient; fourth, the innovation culture and common vision are absent: innovative behavior lacks a continuous driving force. In response to these problems and the formation logic of the synergistic system, this article designs a four-stage cultivation system of "system construction—internal synergy—competition screening—cultural infiltration". The first stage involves building an open system by establishing a cross-border knowledge input mechanism and creating cross-disciplinary communication scenarios, breaking the closed state of the editorial department and injecting external vitality into innovation. The second stage involves creating conditions for self-organization by setting up innovation incubators, thematic project systems, and platforms for free connection and cooperation, stimulating the internal motivation of editors. The third stage establishes competition and cooperation mechanisms by implementing internal creative competitions, strengthening external benchmarking analysis, and establishing a tolerance mechanism to allow high-quality ideas to stand out in healthy ideational competition. The fourth stage cultivates an innovative culture atmosphere by shaping an "encouraging exploration, tolerating failure, and pursuing excellence" order parameter, and through benchmark-setting and optimized incentive systems, making innovation shift from individual behavior to the default behavioral norm of the collective. To ensure the effective implementation of the cultivation system, this article further proposes three safeguard mechanisms. First, establishing a synergistic evaluation mechanism that breaks the traditional workload-based assessment, adds multi-dimensional indicators such as synergy participation and the influence of innovative outputs, and links the evaluation results with professional title promotion and salary rewards. Second, improving the resource safeguard mechanism by setting up a synergistic training special fund, building a synergistic resource library containing an expert think tank, a course library, and a network of practice bases, and providing stable material and intellectual support. Third, establishing a communication and feedback mechanism, through institutionalized review meetings, multi-dimensional dynamic feedback channels, and closed-loop management processes, transforming the cultivation system from a static plan to a continuously optimized living organism. In conclusion, the article holds that the innovative thinking and capabilities of academic journal editors are not a simple manifestation of individual talent, but the joint product of the synergistic cultivation system.