The purpose of this paper is to propose a solution to a problem of modeling the transport flows in mechatronic systems with purposeful objects. The authors offer a structure of intelligent intersection, which could give highest priority to public transport driven by electricity in complex situations. The intelligent intersection includes a subsystem of intelligent Software Agents that interact with executive subsystem implemented by technical resources such as traffic lights. An opportunity of using the intelligent agents for traffic lights switching decision-making is considered for different situations on the intersection. Purposeful objects are objects which purpose their aims and which are not under control of mechatronic systems. The authors offer a generalized algorithm for management of transport flows in mechatronic systems interacting with purposeful objects and describe an experimental approbation of the model to assess the algorithm’s effectiveness.