Organized research constitutes the foundational pillar for high-level scientific and technological self-reliance, whereas non-consensus innovation serves as the critical wellspring of original discovery and disruptive technologies. Their deep integration offers a core pathway for resolving a fundamental dilemma: organized research tends to privilege consolidation over originality, while non-consensus innovation frequently operates in isolation from systematic support. Employing a multi-case comparative design anchored in representative cases from the United States, and Europe, this study moves beyond the binary opposition pervading existing literature. We construct a VERO analytical framework—encompassing value vision, dynamic evaluation, stepped resources, and flexible organization—to uncover the coupling mechanisms across these four dimensions and to dissect how non-consensus innovation survives across diverse governance models and developmental stages. Accordingly, the paper proposes a research management system commensurate with non-consensus innovation. By designing coherent institutional schemes anchored in the VERO framework, it provides both a theoretical foundation and a decision-making reference for facilitating major original breakthroughs and optimizing the governance of China’s National Innovation System.