Smart city is a multidimensional phenomenon consisting of multi-level stakeholders that interact and change in time and space, and despite the expansion of studies, the lack of focus on the governance model to shape and strengthen the urban innovation ecosystem in harmony with the context is noticeable. In this regard, the aim of the research is to provide a conceptual-explanatory framework for analyzing the smart city in the urban innovation ecosystem and its comparative study in three leading cities with different contexts. For this purpose, the reinterpretation and integration of the six-helix model of innovation in interaction with the context and governance mechanism was used to provide a conceptual framework. In general, the aim of innovation governance is a set of institutional, political, technological, etc. mechanisms that focus on achieving the goals of the smart city through the six-helix of innovation. The present study was conducted with a qualitative method and documentary strategy and case study and presented the applicability of the conceptual framework in three cities with diverse governance and context (Singapore, Shanghai and Amsterdam) with comparative text analysis. The findings indicate that the different input of each city played a decisive role in shaping the management strategy. So that in Singapore with a centralized structure, a combination of technocratic and platform-based approaches with adaptive packages was used, in Amsterdam with bottom-up policymaking, a platform-based approach was used, and in Shanghai with a centralized government, a technocratic approach with government transparency was used. Finally, the ISO conceptual framework (input-strategy-output) was presented with the interaction between outputs, inputs and strategies and the possibility of conceptual feedback as an analytical lens for more informed decision-making. Based on this, it can be concluded that to realize a successful smart city, governance strategies must adapt to the innovation ecosystem of each context. Because urban issues with a common nature in different contexts require their own appropriate strategy and technology. Also, the complementary use of these approaches with cultural and popular support can lead to operational added value to achieve a smarter and more sustainable city.