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The innovation value chain is an effective tool for analysing innovation activities and reflects the process of value creation and increase in innovation activities. From the perspective of innovation value chains, we divided patent innovation activities into three stages: knowledge innovation stage, applied research stage and patent commercialization stage. The panel data from 64 universities directly managed by the Ministry of Education from 2009 to 2017 were used and several conclusions were drawn: 1) In the initial stage of knowledge innovation, the fundamental research fund plays a crucial promoting role, and knowledge innovation achievements are mainly published academic papers. 2) In the applied research stage, the knowledge innovation in the early stage and the fund investment in R&D activities have a significant positive effect on the patent output of universities, but the personnel investment has a negative effect. 3) In the final stage of patent commercialization, preliminary research results have a positive impact on patent commercialization, whose marginal effect depends on the industry-university-research relationship, external competition and reputation of the university. The evidence showed that there is a feedback channel between university patent commercialization and knowledge innovation, and new knowledge generated by the interaction with the outside world in the process of patent commercialization was transmitted to the subject of knowledge innovation through this channel, forming a virtuous dynamic cycle. By analysing the driving factors of the value chain of patent innovation in colleges and universities, we provided empirical evidence for the operation mechanism and policy formulation of college patents in China. [ABSTRACT FROM AUTHOR]