The paper dedicates in commemoration of K.A. Bagrinovsky, known scientist, doctor of economic sciences, professor. His thesis was theoretic problems of mathematical modeling and operation of economy. His works in the operations research, the methods making decision, the simulation were received in scientific world. The analysis and the modeling of the mechanisms for scientific and technological development for the production systems of different level in economic hierarchic both centrally controlled economy and making mechanism were conduced by Bagrinovsky in CEMI RAS. The paper presents the investigations (2001–2015) of the analysis and the simulation of the different mechanisms of the innovational activity. It also discusses the methods of the development the complex of the simulation models. In a sense simulation modeling is the science and the art as the selection of the salient parameters for the construction model, intake simplification, the computer experiment and the making decision based on scarcity of accuracy models rest on the heuristic power of men: the practical trial, the intelligence and the intuition. K.A. Bagrinovsky introduced the considerable endowment in the development of this direction for economic and mathematical investigation.The principal object was to show that the relationship between the innovational policy and the technological structure, scientific research sector and the introducing of the progressive production and the organizational structure is obtainable by the models. The character of these relationships may be to use in control of the parameters for the modernization economic. The construction simulation models and the experimental computation analysis were presented the investigations the different mechanisms of the innovational development ant the variants of the estimation have been accomplished on the modeling level by the computer experiment.