Cities are critical research subjects in carbon neutrality, considering they produce more than 70% of greenhouse gas emissions and their crucial role in taking climate actions. The pathway towards a greener society requires consensus, intelligence, and actions among global cities as a network of carbon neutral cities (CNC). Considering cities as complex system-of-systems, synergy among various sub-systems can create co-benefits through the progress towards carbon neutrality. Large volume, velocity, and variety of urban data provide new opportunities for quantifying, analyzing, and visualizing environmental–social–technical dynamics in urban systems. Rich data resources, advanced analytics, and climate actions collectively enable urban intelligence by leveraging data from heterogeneous sources with different spatial granularity and temporal frequency. Such intelligence can promote synergy across sub-systems and domains to support more responsive, precise, proactive planning, policy, and managerial actions. With a discussion on future innovation in urban intelligence for CNC, this paper presents conclusions on how urban intelligence can promote a smarter and greener society.