With rapid changes in technology, knowledge innovation has become more and more complex. Complex partners facilitate knowledge creation and innovation in complex problem-solving. Relying on R&D cooperation with forerunners, latecomers can acquire new knowledge factors and new ideas and use them to create new knowledge. This study demonstrated the knowledge innovation mechanism based on linkages between periphery knowledge and core knowledge with knowledge map theory and set methodology. A case of R&D cooperation between latecomers and forerunners was introduced to verify this mechanism. The results show that latecomers could share forerunners’ periphery knowledge in R&D cooperation through formal and informal interaction and acquire the core knowledge factors in periphery knowledge based on the linkages between them. With these core knowledge factors, latecomers integrate them into their internal knowledge system and create new knowledge. By analyzing the linkages between periphery and core knowledge factors, this study creatively demonstrates the knowledge innovation mechanism in knowledge linkage perspective. It deepens the understanding of R&D cooperation between latecomers and forerunners and expands the focus of knowledge innovation theory. This study provides a new insight into latecomers effectively activating internal and external knowledge resources through R&D cooperation.