The innovation economy is the main direction for Russian’s regional development. It is important to understand organizations that utilize new technologies will determine the significance of innovations. Innovation is changing under the influence of society—the basis for the development of the society is knowledge transfer, and this is one of the most important tasks of the higher education system. In this regard, universities can be considered a factor in innovative development. In this article, the authors hypothesize a link between regional and university indicators. We assume that universities, as part of the regional innovation system, affects the effectiveness of this system. We believe that it is necessary to single out a system of indicators that can be used for analysis, which allows us to determine the efficiency of the region in terms of contribution of universities to its development—because, at the moment, there is no official methodology. The purpose of this study is to determine which indicators are significant for assessing the efficiency of the region, taking into account the activities of university complexes. We will evaluate the efficiency of regional innovation in the region using a data envelopment analysis (DEA). The research objects, or decision-making units (DMU), will be represented by 85 regions of the Russian Federation. A complex of universities operates in each region, and there is a list of socio-economic statistical indicators based on their performance over the past years. There are similar statistical results on the innovative activity of the regions. Thus, we will use the indicators of the complex of universities in the region as initial resources for analysis (2011), as well as indicators of the innovative development of the region as a result of the introduced resources (2018). A time lag of six years is justified by the end of the crisis, and the many factors affecting the activities of universities and regions. For example, increased funding for scientific activities of universities encourages small innovative enterprises within universities. As a result, we were able to identify the level of efficiency, and identify factors that are of greater importance in the resulting model. The findings of the study highlight the importance of educational organizations in the regional innovation system, and encourages alternative interactions between universities and the region, such as joint research and development, training of qualified personnel, and other channels.