This work presents organization, architecture and synthesis as well as analysis of the reconfigurable heterogeneous parallel processing system. Reconfiguration takes place on two levels of the connection network: physical and logical. For its implementation, passive multi-channel optical networks were used. Due to its dynamic nature, the system is designed to handle computational and communication load of an explosive nature and is addressed in the first place to the production sphere of economy. The dynamically combined connection network not only prevents traffic bursts, but also based on the physical and logical circuit commutation gives the possibility of adapting to the existing traffic pattern. Although the described solution is addressed to the optical transmission environment, its effective functioning in the Ethernet networks with circuit switching and partly in wireless networks has been confirmed empirically. The theoretical foundations were verified in the design and construction of a reconfigurable super-microcomputer and the intelligent system detection of attacks addressed to industrial Internet.