Purpose It is widely accepted that enterprises obtaining academic discoveries through R&D collaboration improve their innovation performance. However, it is not necessarily true in emerging economies, such as China and post-socialist countries in Europe. The purpose of this paper is to fill the gap by investigating how R&D collaboration between industry and academia (i.e. universities and research institutes) affects the industrial innovation performance; and whether and how intermediaries moderate their relationships. Design/methodology/approach This paper constructs the research model according to the knowledge production function, and the pooled ordinary least square regression is used to verify our hypotheses. Findings Evidence from a sample of Chinese industrial enterprises in thirty provinces spanning from 2009 to 2014 suggests that R&D collaboration with research institutes (CWR) is positively related to innovation output, while R&D collaboration with universities (CWU) exerts negative effect on innovation output measured by sales revenue of new product (NPSR). The significant moderating role of technology transfer institutions is confirmed in the negative relationship between CWU and NPSR. Originality/value This paper empirically examines the moderating role of intermediary organisations in academia–industry cooperation and industrial innovation, and has practical implications for the government to formulate policies to improve the quality and effectiveness of cooperation between academic and industrial sectors. These results vary in inland and coastal areas, which suggest the policy makers to formulate policies according to local conditions not only in China but also in other countries, like European countries.