The sustainable development of deep industry-university-research integration has emerged as a strategic imperative within the global innovation ecosystem landscape. Existing studies often treat policy, market, and social capital as isolated factors, overlooking their configurational interplay and lacking an explanation of the sustainable development of deep industry-university-research integration in China’s unique institutional setting. This study integrates configuration theory and innovation ecosystem theory and employs fsQCA to examine 10 representative industry-university-research collaborative innovation cases in China. The findings reveal: A distinct “embedded authoritarian synergy” governance architecture characterizes China’s deep industry-university-research integration, where state-led strategic directives are dynamically coordinated with market-based contractual mechanisms and socially embedded relational networks. Sustainability is achieved through three equifinal configurational pathways: state-led mission-driven, policy-market adaptive, and policy-relational contingent. Each pathway entails specific institutional tensions, such as decoupling between policy design and implementation, weakening endogenous drivers, or erosion of social capital. Theoretically, this study advances innovation ecosystem scholarship by proposing a configurational framework and the “embedded authoritarian synergy” model to explain how state, market, and societal logics interact in a hybrid institutional context. Practically, it offers policymakers a diagnostic tool for designing differentiated governance strategies tailored to regional institutional endowments, thereby guiding industry-university-research collaboration toward economically transformative, socially inclusive, and environmentally sustainable development goals.
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