A method of determining flexible manufacturing system performance (throughput capacity) based on identifying elementary controlled events that occur during FMS operation and controlling this flow based on Shannon approach to evaluation of the quantity of information required for control is proposed. The behavior of the main FMS elements in the manufacturing process is suggested to be described using three types of random flows of square pulses – state, availability and propagation flows. The proposed mathematical model enables to choose the optimum relationship between FMS power margins, parts and tools supply and throughput capacity.