The relevance of the research is due to the accelerating transformation of economic systems under the influence of digitalization and global challenges such as climate risks, geopolitical instability and technological fragmentation. At a time when digital ecosystems are becoming a key driver of innovative growth, there is an urgent need to develop adaptive models for assessing their sustainability, taking into account not only classical ESG parameters, but also the specifics of the knowledge economy. The aim of the research is to form a theoretical and methodological framework for assessing the sustainability of digital ecosystems at the enterprise level and inter-organizational networks, taking into account innovation activity, cognitive complexity and digital maturity. The research uses a systematic approach, comparative analysis, entropy weighting method, Lyapunov method, as well as elements of predictive analytics and machine learning to assess stability dynamics. The results of the study include: updating conceptual models of sustainable development, taking into account the transformation of the environmental component into an "innovative" or "digital" one; the proposal of a composite index of sustainability of the digital ecosystem (CIDE); the development of two tables of metrics – on aspects of sustainability and on levels of analysis. In conclusion, it is emphasized that the sustainability of digital ecosystems in the knowledge economy is impossible without synergy between technological maturity, innovation policy and social responsibility, as well as without taking into account regional and sectoral specifics, especially in developing regions such as the Republic of Dagestan.