The launch of the Eurasian Economic Union which united the Russian Federation, Belarus, Kazakhstan and Armenia is one of the basic steps to create a united economic space. It will provide not only free movement of goods and services, but also will give opportunity for free share of creative activity results, and use funding and specialists from different countries for its implementation. For Kazakhstan, the formation of the integrated innovation system in the future will significantly diversify the economy and balance it reducing the dependence on the extraction and export of raw materials. This study is based on the methods of system analysis and institutional analysis of the national innovation systems functioning, including the countries participating in the integration associations. The scientific and innovative activity as basic type of creativity for modern market economy resulting in the development of new modern productions, emergence of new goods and services, increase of an added value and its multiplicative effect for the whole economy requires involvement of a more increasing number of resources, use of cooperation opportunities and integration to achieve the maximum competitiveness at the present stage to development. The joining efforts directed on formation of concepts and ideas of scientific-innovative projects, attraction of financial sources of different types from the different countries, implementation of research results and their development on the platforms in various countries in different economic conditions, formation of the international projects in the sphere of goods production and services provision can be referred to such resources.