Against the backdrop of intensifying global environmental challenges, the fostering of green innovation and sustainable development in cities is considered pivotal to China's high-quality development. The dual pilot policy of Innovative Cities and New Energy Demonstration Cities was investigated. A difference-in-differences model was applied from a collaborative governance perspective. The interplay between technological innovation and energy transition was analyzed to understand its role in urban green innovation ecological construction. The dual pilot policy is found to significantly and persistently enhance urban green innovation capacity. This effect is observed to operate through three key mechanisms. Firstly, public environmental awareness is raised, which expands market demand for green technologies. Secondly, corporate innovation is stimulated and talent potential is unleashed, thereby optimizing the allocation of innovation resources. Thirdly, industrial upgrading is advanced to foster endogenous growth in the green economy. Regional heterogeneity analysis indicates that the policy's effects are more pronounced in eastern regions, non-resource-based cities, and cities with strong knowledge-dissemination capacities. Furthermore, spatial econometric results reveal that while green innovation efficiency is effectively boosted in pilot cities, a "regional siphon effect" may also be created. Technology and resources are diverted away from non-pilot cities, which may potentially hinder their development. Conventional single-policy evaluations are moved beyond by uncovering the synergistic effects of integrating technological innovation with energy transition. New empirical evidence is provided for collaborative governance and green innovation theories. Valuable insights are also offered for global sustainable development policymaking, particularly in balancing efficiency gains with regional equity.