Exploring the pathways to high-quality development for new R&D institutions is of strategic importance for enhancing the overall effectiveness of the national innovation system and achieving greater self-reliance in science and technology. Currently, the majority of China’s new R&D institutions face the dual dilemmas of vague functional positioning and idle institutional advantages, which constrain the effective release of their innovative vitality. Grounded in innovation ecosystem theory, this study constructs an integrated analytical framework comprising a “goal layer” and a “behavior layer.” Following the resource mobilization process of “element unit → element flow → element flow bundle” under core objectives, an exploratory multi-case study of five typical new R&D institutions that have achieved high-quality development in China is conducted using grounded theory procedures. The findings reveal four core pathways: niche construction, key actor leadership, internal governance innovation, and external collaboration empowerment. The effectiveness of these pathways is highly contingent upon their dynamic alignment with the functional positioning of basic, applied, and comprehensive institutional types, thereby giving rise to the intrinsic logic of categorized governance. Based on these findings, a process theory is constructed that takes strategic positioning as the starting point, top-tier talent as the engine, endogenous drive as the core, and external empowerment as the support. Finally, the study proposes a set of governance recommendations, including establishing a classified ecological niche layout mechanism based on strategic positioning, constructing a categorized talent evaluation and incentive system centered on contribution orientation, promoting differentiated internal governance reforms along the main line of classified deregulation, and building external collaboration networks in a classified manner with platform empowerment as the lever. These proposals provide a theoretical foundation and practical guidance for facilitating the shift of new R&D institutions from quantitative expansion to a qualitative leap during the “15th Five-Year Plan” period.