For the effective functioning of economic mechanism of innovative structures the model of the logistic system and algorithm of its functioning has been offered, the structure of financial streams, ways of its motion and management mechanism have been described. It will be instrumental in an analysis, estimation and prognostication of the states of financial streams, preparation and making decision after the states of input and process resource streams, output and market food streams, in preparation and making decision on a management the states of both resource and food streams.