The article considers the forms and conditions of interaction between the participants in the innovation process, the specialties of creating and developing the organizational system of technology transfer in the member countries of the Shanghai Cooperation Organization (SCO). Based on the analysis of transfer systems operating in various countries (China, Kazakhstan, Kyrgyzstan, Russia, Tajikistan, Uzbekistan), the authors highlight key and most promising areas for the development of integration of the scientific, educational, industrial spheres and the state in order to form special mechanisms for organizing innovative processes that ensure effective interaction between all its participants. The purpose of the article is to analyze the national innovation systems of SCO member countries, since each of these countries has gone its own way of innovative development, justified by regional characteristics (climatic, cultural, socio-economic, etc.). As basic research methods we used system approach, comparative and statistical analysis of indicative values of innovation and technological development of the SCO member countries.The authors conclude that it is necessary to create an organizational system based on the integration of state institutions, science, business and education in the Shanghai Cooperation Organization member countries in order to form competitive high-tech products, improve the export structure by increasing the share of innovative products in it and reducing the raw materials orientation, and increase the status of countries in the world technology market.