At present, issues of ecosystem self-organization and the mechanisms for their sustainable development have been insufficiently explored in academic literature. The key idea of our research is that for enterprises interacting in different industries based on a network partnership, a special tool is needed to ensure the openness of interaction between participants in the transfer of knowledge, technology, information, and resources. The authors argue that the development and practical implementation of a cross-sectoral digital ecosystem platform will allow for the synchronizing of the scientific and technological progress of several industries, making the most effective use of the synergistic effect from the interaction of ecosystem actors and ensuring the transparency and openness of the ongoing processes therein. The authors demonstrate their propositions with the example of unmanned aircraft system (UAS) industry. The proposed model and mechanism of cross-sectoral interaction can be replicated in different technological niches, such as robotics, neurotechnology, quantum technologies, etc. The conclusions arising from the conducted research provide scientists, government bodies, and decision-makers with the necessary information for a better understanding of practical mechanisms and tools that allow for the implementation of self-organization and sustainable development in modern innovation ecosystems.