The structure and activities of science, technology and innovation organizations should be reviewed in planning for change in accordance with (a) a framework operating model, (b) principles of organizational structures and (c) value chains in order to identify (1) areas of inefficiency, (2) the existence and maturity of chain links as well as (3) gaps with best practice. The operating model of organizations, whose support, development and effectiveness are influenced by legislation, budget and external factors, includes many components, from management policy to culture. Changes in organizational charts together with renaming of departments sometimes look like promising reforms. However, in any case, values brought by organizations should be put on the agenda. Social effect of science, technology and innovation as a contribution to public good or a measure of the social good extend to groups in society or to the whole of society both directly and indirectly, for example, through other values and social mechanisms of influence. In this article, the following typology of values is used in the context of the innovation ecosystem and discussions on public good: internal, economic, social and humanitarian ones. The last three values are often generalized by the term “impact”. Internal values of science and technology express the essence of development that knowledge is built on knowledge, and thereby increase the level and readiness of organizations. We consider links in the value proposition chains produced by these organizations, from planning to legal support management. Current national macro factors that influence them are formulated. The contemporary generation of the innovation ecosystem in the Republic of Kazakhstan is characterized by a lack of a group of elements that determine national internal and external goals, ways to achieve them, as well as monitoring the results of activities and impact. This article aims to formulate and study the linking of management at the level of the principles of the organizational structure and the framework operating model to the values at the level of the introduced typology, which are created in a certain way by science, technology and innovation organizations. In terms of research and practical significance, this allows for a detailed review, identification of areas of inefficiency and gaps with best practice. And then, by formulating and implementing initiatives, this allows to increase their capabilities and effectiveness taking into account the ambiguity and delayed nature of results of scientific, technological and innovative activities, as well as specific external national and international factors that influence organizations. Comparing value chain links to the typology of values, we have identified a specific distribution of their influence of on the types of these values. In terms of academic and theoretical significance, this study also attempts to reveal contradictions between resulting and procedural values in science, technology and innovation organizations by examining the development of value chains and the context of public good.