The article examines the issue of improving the efficiency of complex systems management through the use of knowledge-based methods and technologies. The article emphasizes the need to revise traditional approaches to scientific research and knowledge management by introducing a transdisciplinary paradigm and artificial intelligence to achieve sustainable development and knowledge evolution. The authors try to solve the problem of management in the face of uncertainty and incomplete information, which is typical for such systems. The methods of integrating knowledge from different fields to create an integrated management system are considered. The basis of management is the holarchic structure, which organizes the system in the form of a hierarchy of holons. Each holon has a specific role and knowledge, which ensures the flexibility and adaptability of the system. The study also uses self-organization and learning methods to ensure continuous improvement of the systemʼs functioning. The article discusses the requirements for knowledge-based management systems, such as flexibility, adaptability, data and knowledge integration, learning and self-organization, transparency of decisions, and resilience to errors and failures. The findings of the study emphasize the importance of implementing knowledge-based approaches in the management system of complex facilities. This allows to increase the level of adaptability and stability of management, which is critical in todayʼs environment of dynamic development of technology and knowledge. The proposed methods can be applied in various fields, which makes them universal and useful for a wide range of scientific and practical tasks, providing a high level of adaptability, efficiency and stability of complex objects management, taking into account modern requirements and challenges.