Against the backdrop of the current complex and volatile international landscape, establishing a highly symbiotic innovation ecosystem based on International Joint Research Centers is highly beneficial. This approach will further enhance the innovation capacity and sustainable development capabilities of China’s research institutions. This paper employs the TOE (Technology-Organization-Environment) framework and builds upon the concepts of symbiosis and innovation ecology. It systematically examines the factors influencing the strength of symbiosis within innovation ecosystems from technological, organizational, environmental, and safeguard mechanism perspectives. It is demonstrated that constructing a highly symbiotic innovation ecosystem using the TOE framework can significantly improve the R&D capabilities, management efficacy, and resource integration capacity of International Joint Research Centers. This paper also explores approaches for building such symbiotic innovation ecosystems within International Joint Research Centers, including specific implementation strategies and relevant policy recommendations, providing references for enhancing international science and technology management practices.