The new wave of technological revolution is driving a paradigm shift in scientific research toward organized research models. The key to translating organized research from theoretical exploration to practical efficacy lies in the allocation and synergy of innovation elements. The Regional Innovation and Development Joint Fund as a typical practice of scientific funds under organized research, serves as an important benchmark for evaluating the transition from theoretical exploration to practical application in organized research. This study takes the Shandong Regional Joint Fund as an example and uses Necessary Condition Analysis (NCA) and fuzzy-set Qualitative Comparative Analysis (fsQCA) to investigate how different configurations of factors influence project effectiveness from a configurational perspective. The study aims to explore how scientific funds drive the improvement of their effectiveness through the configuration matching of multiple elements under organized scientific research. We try to open the 'black box' of improving the efficiency of organized scientific research. The study finds that: (1) The improvement of scientific fund efficiency depends on the coordinated matching of multiple elements, and a single element does not constitute a necessary condition for high efficiency. We found that among elements such as the project leader's (PI) ability, PI age, team heterogeneity, team collaboration, disciplinary foundation, and institutional reputation cannot individually serve as necessary conditions for the high efficiency of regional joint funds. The effective way to improve the efficiency of scientific funds is the complex combination of multiple conditions. (2) Disciplinary foundation is a key factor affecting project effectiveness and play a rigid supporting role. With the advancement of Double First-Class Initiative in China, first-class disciplines have strengthened their core position in resource aggregation and innovation ecosystems. The finding that disciplinary foundation serves as a critical support for project effectiveness not only empirically validates the "Matthew Effect" in scientific research but also demonstrates the rationality of the Double First-Class Initiative in China being discipline-based from the perspective of performance. (3) There are multiple configurational pathways to enhance the effectiveness of regional joint scientific funds: Resource-driven young leader type, Discipline-supported team growth type, Government-Industry-academic collaboration type. Among these, the Resource-driven young leader type is the most common. We also found that there is a certain substitution effect between different elements. For example, under a strong discipline, elastic factors such as PI capabilities, team collaboration, and institutional reputation can be substituted through combination and replacement. This finding provides an important basis for the allocation of scientific research resources. These elements can be reconfigured through combinatorial optimization to enhance project efficacy. This paper breaks through the limitations of traditional single-factor analysis of project efficiency. It reveals the impact of the combination and matching of scientific research elements in organized scientific research from a configurational perspective, providing a new paradigm for scientific research management under the complex system perspective. The conclusion that "disciplinary foundation is a rigid support for enhancing efficiency, and elastic elements exhibit conditional substitution effects" demonstrates that organized scientific research is the result of the synergistic matching between rigid resource support and elastic elements. This not only provides an important basis for optimizing the allocation of scientific research resources in practice, but also solves the "paradigm code" of organized scientific research from theoretical exploration to practical verification.