A comprehensive framework for designing, analyzing, and managing critical information infrastructure within a smart city digital ecosystem has been developed using Moscow as an example. The study introduces entropy-based methodological approaches, a hybrid decision-making strategy combining compensatory and non-compensatory methods within the Markov decision-making process, and a method for structural optimization of neural networks. A new intelligent decision support system has been developed for automatic verification of design models and prevention of false data injections. The results highlight the need for multi-perspective analysis (elemental, structural, integrative, communication, historical) to ensure sustainability, security, and reliability of the city’s critical information infrastructure.