In the face of fierce market competition, enterprises must ensure the competitiveness of their products or services through technological innovation. However, the complexity of technology often surpasses the capabilities of individual enterprises, leading them to deepen cooperation with other organizations. The entities within the enterprise innovation ecosystem depend on each other, collaborate closely, and rely on core enterprises to integrate resources, thereby creating system value and enhancing competitiveness. The purpose of this paper is to explore the process of selecting appropriate ecosystem partners. It begins by providing an overview of relevant concepts, characteristics, selection factors, and methods. Subsequently, it analyzes the roles, resources, and synergy evolution of the entities within the ecosystem. An evaluation system encompassing operation, core, synergy, and development capability is then established. This system comprises 16 indicators, including organization scale and reputation, and is accompanied by a hierarchical evaluation model. Finally, the validity of the evaluation system is confirmed through empirical analysis, utilizing the Analytic Hierarchy Process (AHP) and the fuzzy comprehensive evaluation method.