In the conditions of intense competition, of products of the Russian enterprises which determine rates and quality of economic development approaches to formation of business systems become the most important factor of improving competitiveness of the enterprise. Tools (methods and techniques) which are the cornerstone of the increase in efficiency of these systems allow to increase quality of products or services, to reduce expenses, to improve discipline of delivery without essential investment expenses. At the same time, various companies introduce these tools differently, in various sequences and combinations, which sometimes results in low effectiveness of these tools. It is connected with the lack of the formalized technique of the tool kit optimization increasing efficiency of a business system which will allow to provide the maximum effect in the conditions of restrictions for human and temporal resources. For this reason, development of a technique of the tool kit optimization to increase efficiency of a business system on the basis of maximizing the effect of the transformational project for a certain enterprise is represented a relevant scientific task. The business system of the enterprise involved in a multi-industry cluster structure acts as an object of the research. The research objective is the development of a technique of the tool kit optimization to increase efficiency and functioning of a business system. To solve this task, the authors proposed to use the methods of mathematical optimization. To form a criterion function of the optimizing model, the authors conducted a research on the efficiency of the business system tools on the basis of a regression analysis of results of 170 projects implemented by various enterprises in a multi-industry holding. To form restrictions, the authors evaluated statistics on duration of tools formation. COBYLA method was used to solve the problem of optimization with restrictions. The developed technique allows to increase the efficiency of implementation of transformational projects in various companies (for example, in terms of decreasing production costs) by 7–10% due to optimum selection of tools increasing the efficiency of a business system.