Economic integration is an important engine for development of national economies. Given that the dynamically developing innovative business is a core of the competitiveness of a modern economy, the authors suggest their view on the options and mechanisms for the development of Kazakhstan's innovative business within the framework of the Eurasian Economic Union (EAEU). In the article on the basis of the conducted in 2015-2017 studies of options and prospects for creation and development of the unified supra national innovation system of the EAEU, the authors briefly describe the key problems of the Kazakhstani innovation business and the tools and option provided by the EAEU to innovative companies in Kazakhstan. We also suggest three basic mechanisms on which the EAEU unified supra-national innovation system should be built: mechanism for information exchange on current innovation projects; mechanism for access to resources; mechanism for creating and supporting joint innovation enterprises and firms. The proposed mechanisms together with the expanded scheme of the innovation process, illustrate the new content of cooperation between innovation companies and subjects of innovation infrastructure within the framework of the EAEU; they also allow to get a sense of the additional options that are provided by the creation of joint ventures and enterprises.