[Purpose/significance] Exploring the key issues of interdisciplinary research collaboration based on ecosystem theory can systematically clarify its analysis perspectives, influencing factors and stakeholders, so as to better layout and promote practice, and accelerate scientific innovation. [Method/process] The study analyzes the core connotation of ecosystem theory, explores its relationship with interdisciplinary research collaboration operation, constructs interdisciplinary research collaboration operation ecosystem framework, and refines the key issues. [Result/conclusion]As for individual-oriented guarantee conditions, it is necessary to improve interdisciplinary research collaboration platform and academic conferences to stimulate collaboration enthusiasm and enhance collaboration possibility; as for collaboration networks, emphasis is placed on the compatibility of partners, trust relationships and interest coordination mechanisms to ensure cohesion and sustainable development; external support involves multi-level promotion policies,research project review and funding mechanisms, adaptability and flexibility of discipline systems.