The transition to clean energy in China’s traditional industrial regions requires technological substitution and fundamentally restructures the relationship among the state, the market, and enterprises. This study examines the influence of industrial legacy and governance structures on clean energy innovation in Northeast China, with a primary focus on Jilin and comparative analyses of Liaoning and Heilongjiang. Using patent data from 2000 to 2025, we employ Shannon entropy, location quotients and logistic modeling to analyze innovation dynamics across temporal, structural, spatial and institutional dimensions. Our analysis reveals three governance regimes reflecting different industrial legacies and identifies a significant mismatch between resources and innovation: resource-rich cities generate a low number of patents relative to their resources. A high invalidation rate suggests maintenance deficits in publicly funded innovation. These patterns imply that governance arrangements may contribute to the structural weaknesses observed in regional innovation systems. We propose a differentiated strategic framework adapted to the industrial legacy of each province, suggesting that old industrial bases require reforms addressing both resource endowment and institutional capacity. Our findings have implications for regional innovation governance in resource-dependent economies undergoing energy transition.