The necessity of developing transport and logistics processes based on their digital and intellectual transformation, representation of transport and logistics facilities in the form of cyber-physical systems is shown. The category of “intelligence” is analyzed and the identification of various types of natural intelligence implemented in Nature is substantiated. On this basis, the concept of “nature-like decision-making mechanisms” is formulated, which include: human-like, animal-like, insect-like mechanisms, as well as mechanisms that arise as a result of the bioelectric activity of the intelligence carrier. Mathematical constructions adequate to each given decision-making mechanism are described. The mechanisms of effective decision-making in various situations are classified and investigated, differing in the required speed of decision-making, the level of uncertainty and noise of the data used, and the psycho-emotional status of the decision-maker. The conditions and limits of applicability for this purpose of the tools of the theory of active systems, finite and cellular automata, neural networks, model constructions of the theory of fuzzy sets and neuro-fuzzy modeling are defined. The technologies of translating natural intelligence to a machine taking into account the features of the object under research, including those modeled by the algorithms of Mamdani, Tsukamoto, Larsen, Sugeno are systematized. The modeling of seamless interactions of agents in the design and process organization of work of a complex transport facility by means of finite and cellular automata is updated.