The key technology self-reliance of intelligent manufacturing of complex products is the only way to solidify the foundation of localization in the manufacturing industry and achieve technological self-reliance. Although digital ecosystems can efficiently aggregate external resources for enterprise technological innovation, internalizing them as independent innovation drivers remains a key challenge. Therefore, exploring how to optimize the configuration of digital ecosystems and strengthen core technology self research while integrating resources is an urgent practical problem that needs to be solved. Based on organizational orchestration theory, key conditions are extracted from the “structure relationship” dimension, and a “orchestration implementation” configuration model is constructed. Based on survey data from 89 enterprises, fs/QCA analysis shows that there are four digital ecological orchestration strategies that drive the autonomy of key technologies, namely agglomeration symbiosis strategy, niche dependence strategy, process transformation strategy, and heterogeneous complementarity strategy. Various strategies map the key technological breakthroughs of enterprises in different industrial sectors, requiring the construction of differentiated structures and relationship linkage models in digital ecosystem architecture design and resource collaborative allocation. These strategies are sequentially adapted to the clustering and collaboration of supporting process technologies, the dislocation dependence of precision machining technologies, the complementarity of assembly control technologies, and the cross-border cross technology transformation, which are typical scenarios for four types of intelligent manufacturing applications. This article has practical significance for enhancing the autonomy and controllability of key technological innovation in enterprises and constructing a new pattern of ecological development in the intelligent manufacturing industry.