The characteristic of innovation activity of an enterprise are quite complex and their informative analysis based on heuristic methods is difficult. This predetermines the need to apply different models and modeling methods. The economic-mathematical model of the innovation strategy of an enterprise should include, from our point of view, a description of the enterprise as a subject of innovative activity and the mechanism of its new development. It is assumed that the use of economic and mathematical models allows to obtain new knowledge about innovative development of an enterprise. The article is devoted to the study of the problem developing mathematical models of process optimization, modeling innovative development of enterprises in Kazakhstan. Analysis of the existing scientific tools for modeling innovation development of various economic systems has led to the conclusion that for its use in modeling the innovative strategy of enterprise, it is necessary to clarify the specified toolkit based on specifics of this type of an enterprise. It should be born in mind that modeling should be preceded by the stage of analysis of innovative activity of an enterprise, including not only current situation, but also possibilities of its transformation in accordance with the goals of the enterprise.