This article presents a new simulation model of an intelligent transportation system (ITS) for the “smart city” with adaptive traffic light control. The proposed transportation model, implemented in the AnyLogic, allows us to study the behavior of interacting agents: vehicles (V) and pedestrians (P) within the framework of a multi-agent ITS of the “Manhattan Lattice” type. The spatial dynamics of agents in such an ITS is described using the systems of finite-difference equations with the variable structure, considering the controlling impact of the “smart traffic lights.” Various methods of traffic light control aimed at maximizing the total traffic of the ITS output flow have been studied, in particular, by forming the required duration phases with the use of a genetic optimization algorithm, with a local (“weakly adaptive”) switching control and based on the proposed fuzzy clustering algorithm. The possibilities of optimizing the characteristics of systems for individual control of the behavior of traffic lights under various scenarios, in particular, for the ITS with spatially homogeneous and periodic characteristics, are investigated. To determine the best values of individual parameters of traffic light control systems, such as the phases’ durations, the radius of observation of traffic and pedestrian flows, threshold coefficients, the number of clusters, etc., the previously proposed parallel real-coded genetic optimization algorithm (RCGA type) is used. The proposed method of adaptive control of traffic lights based on fuzzy clustering demonstrates greater efficiency in comparison with the known methods of collective impact and local (“weakly adaptive”) control. The results of the work can be considered a component of the decision-making system in the management of urban services.