R&D cooperation is one of the main channels for new knowledge diffusion to create innovation. Therefore, it is important to understand exactly how enterprises use this channel. The purpose of this article is to identify the structure of R&D cooperation determined by both the heterogeneity of partners and the size of organizations. This structure is considered in dynamics. The analysis is based on Rosstat data characterizing the participation in joint R&D projects of innovation-active firms from 2019 to 2022. This approach allows us to find out how the structure of cooperation changes under the influence of crisis. However, unlike most Russian studies, this work also defines the relationship between the choice of R&D partners and the absorptive capacity of organizations in Russia. Differences in absorptive capacities (i.e. abilities of organizations to find, assimilate and apply new knowledge from external sources) largely determine the choice of partners in innovation activities and the results of cooperation. The article finds that despite government efforts the links between science and business are weakening in Russia, as not only small entities but even large companies have largely shifted their preferences to less risky projects. The persistence of such cooperation patterns leads to a decrease or even loss of Russian firms’ capacity to assimilate and use new knowledge to create radical innovations. Consequently, measures are needed not only to maintain the scale of R&D collaboration, but also to avoid negative changes in their structure. Such measures should also include incentives for enterprises to increase absorptive capacities. Unfortunately, these incentives have received little attention both in the practice of innovation management and in Russian economic literature.