Abstract: Against the backdrop of intensifying global competition in foundational and frontier technologies, original innovation has become a core driver of technological self-reliance and industrial upgrading. The internal mechanisms of original innovation, particularly the interaction between scientific research and technology R&D have gained increasing scholarly attention. While prior studies have preliminarily revealed the linkage between science and technology from a knowledge-flow perspective, systematic empirical evidence on how the two form a sustained, bidirectional positive feedback loop within the original innovation system remains scarce. To address this gap, this study focuses on the new energy vehicle industry, analyzing paper and patent data from 42 enterprises between 2015 and 2024. Using dynamic structural equation modeling (DSEM), we examine the bidirectional evolution paths, mediating mechanisms, and boundary conditions between scientific research and technology R&D. The results show, first, a significant bidirectional causal relationship between firms’ scientific research intensity and technology R&D intensity, forming a stable positive feedback cycle and promoting sustainable innovation. Second, scientific research quality and technology R&D breadth play key mediating roles in this dynamic transformation. High-quality scientific research enhances the authority and systematization of propositional knowledge, thereby advancing subsequent technology R&D. Broad technology R&D, in turn, expands the scope and diversity of prescriptive knowledge, helping to refine scientific questions and focus research directions. Third, cooperation intensity exerts significant cross-level moderating effects: technology cooperation strengthens the mediating path from research quality to R&D intensity, while research cooperation enhances the transformation from technology breadth to research intensity. These findings underscore the vital role of innovation collaboration in knowledge complementarity and resource integration. This study offers three main theoretical contributions. It provides the first empirical validation of the positive feedback mechanism between science and technology in the original innovation system, deepening the understanding of innovation sustainability. It also reveals the mediating role of propositional and prescriptive knowledge in the bidirectional transformation, extending the knowledge-based view into dynamic innovation research. Finally, it clarifies the enabling effect of collaboration at the firm level, addressing a literature gap that has long emphasized macro-innovation ecosystems while overlooking micro-level transformation mechanisms.