The article is devoted to studying the possibilities and conditions for increasing the role of small business entities operating in the science towns territory in the process of forming and developing the regions innovation ecosystem. A bibliographic review of scientific views on interpreting the "innovation ecosystem" concept is carried out; the author's interpretation of the researched definition is proposed, which most widely reveals its actual essence. The criteria for classifying a territorial entity as a "science town" are outlined; the defining role of science towns in forming the region innovation ecosystem as points of its growth is emphasized. The article presents the positive dynamics of the development of science towns in Russia, as well as small businesses as drivers of their development (on the example of Moscow region). In this regard, the experience of implementing programs of state support for small business in Moscow region has been studied; the scale of financial support has been estimated. The factors hindering the innovative development of small enterprises in science towns have been identified. An innovation ecosystem project is proposed, which is formed, inter alia, by strengthening the interaction between its main actors: the business community, the educational environment, the scientific community, science towns corporations, regional authorities. The main advantages of implementing such a project are noted. The principles of the region innovation ecosystem functioning are determined to achieve the goals of increasing its efficiency and competitiveness. The results of the study are of practical importance in terms of the possibility of their application by regional authorities when implementing programs for the innovative development of science towns and regions in general. In addition, the proposed approach to the formation of an innovation ecosystem can be used by entrepreneurs when developing trajectories for their business development.