The purpose of the study is to develop an organizational and economic mechanism for managing the intellectual capital of NGOs in the interests of innovation in the process of transition to activities based on digital technologies and definition necessary conditions for ensure its functioning. The object of the study is the intellectual capital of a research and production organization in the transition to digital technologies. The subject of the study is the system of economic, organizational and social relations that arise in the process of management intellectual capital in processes research and production organization in the interests of innovation. The system of management of IC NPO based on the organizational and economic mechanism is presented, which works in the interests of innovation in the process of transition to activities based on digital technologies, taking into account the necessary conditions for ensuring its functioning.