Introduction of information technologies in almost all spheres of life of the world's population is a global challenge of the present. The task of digitization of all spheres of production is a strategic goal and a national security issue for Russia, since the lag in this field sharply reduces the competitiveness of individual organizations and the economy as a whole. We analyze and classify not only a variety of theoretical provisions about the essence and structure of intellectual capital, but also its new qualities in the context of digital economy. Taking an interdisciplinary approach into account, we consider intellectual capital to be a structured set of intangible factors of production. Such factors help generate revenue to the participants of these relations in accordance with the changing market environment. Analysis of peculiarities of introduction of digital technologies in research and production organizations and clusters is given, requirements to structural and informative characteristics of intellectual capital are determined. A new structural component of intellectual capital (further IC) in the digital economy is social capital. It is independent from other structural components (by the source of formation), but it has significant influence on the remaining components (of the structure). The study has proved that it is necessary to initiate preliminary activities and analyze all the external and internal organizational factors in the development of digital technologies in research and production organizations and in research and production clusters (hereinafter RPOs and RPCs). These factors are as follows: global technological factors of growth; state policy in the field of digitization of the economy and support of enterprises; labor market characteristics that are determined by target education, introduction of digital generation Z to the market, and presence of generation Y in the market (both accustomed to communicative digital technologies at the level of age socialization). The internal organizational factors that influence the development of the intellectual capital of RPOs and RPCs are: change management system aimed at reducing staff resistance, and the corporate culture that must be formed as market-based and administrative. We propose a scoring system as a method of intellectual capital evaluation in order to manage it under digitization. We have developed an organizational and economic mechanism aimed at development and involvement of the IC in the activities of a particular RPO. We have also developed (based on organizational and economic mechanism) a system of IC management (for specific RPOs) that is to be implemented in the process of digitization.