The article discusses the issue of development of method for structural synthesis of large discrete systems with predetermined behavior and dynamic structure. This is aided by combined approach to development of structural synthesis based on simulation modeling, evolutionary methods and mathematical apparatus of Petri nets. The developed evolutionary procedures of system structural synthesis makes it possible to carry out structural synthesis in accordance with predetermined behavior not only by selection of components from elemental base but also by variation of inter-component couplings. The work proposes to apply genetic algorithms adapted to solution of problem of structural synthesis using nested Petri nets. The system component base applied for the synthesis procedure is expressed in the form of models based on Petri nets, the system models obtained by synthesis are estimated by computational experiment, that is, launching of the obtained system models by supplying of vector tuple to the model input and comparison of the tuple from the model output with reference one. Upon adaptation of genetic algorithm for operation with multi-component couplings it is proposed to highlight a separate layer of inter-component bus.