Abstract: In the field of science-based innovation, science-based enterprises bear the mission of commercializing fundamental scientific achievements while concurrently engaging in supplementary research, becoming a tangible driving force for advancing economic and social development. Constructing internal governance mechanisms for science-based enterprises has become a key factor in nurturing innovation capabilities. This paper employs a case study method to systematically explore issues such as the formation logic of internal governance mechanisms, the construction of governance functions, and the expansion of governance boundaries. The discussion encompasses the coupling mechanisms of internal and external factors, leading to the extraction of a theoretical model for internal governance mechanisms of such enterprises. In terms of sample selection, adhering to the principles of representativeness and theoretical sampling, this paper chooses firms listed on Sci-Tech innovation board (STAR Market) that are engaged in the “scientific research and technical services” industry. Subsequently, it further selects biopharmaceutical firms involved in research and experimental development. Through a review of corporate materials, five firms are identified that are engaged in the transformation of basic scientific achievements while concurrently conducting supplementary scientific research. This paper encodes case data in three steps, forming a data structure consisting of first-order constructs, second-order themes, and theoretical categories. Based on this data structure, the paper proposes propositions, discusses the operation of science-based corporate internal governance mechanisms, and ultimately presents a model of coupling mechanisms in internal governance. The study reveals that the dominant logic in the formation and development of governance mechanisms for scientific-based enterprises is centered around “emphasizing original innovation and breakthroughs in core technologies”. In terms of configuring the talent pool for innovative research and development, the core leadership team is centered around individuals with a “scientific background”, supported by an innovative research and development team. Regarding personnel incentive mechanisms, a combination of “short-term compensation incentives” ensuring market competitiveness and “long-term equity incentives” with binding effects is adopted. In the equity arrangement mechanism, a hybrid equity model involving “long-term oriented strategic investors” and “scientists holding significant control rights” is implemented. Furthermore, the governance boundaries are blurred, with diverse governance entities such as “universities, science parks, government, and customers” expanding the governance boundaries of these enterprises, leveraging the coupling effects of internal and external governance mechanisms. The main theoretical contributions of this paper are as follows. Firstly, the paper elucidates the “dominant logic” of science-based corporate governance mechanisms, contributing to an understanding of the cognitive foundation and behavioral logic in the formation process of these governance mechanisms. This fills a gap in previous literature, which only focused on the external behavioral manifestations of such corporate governance mechanisms. Secondly, the paper goes beyond the analysis of the impact of team heterogeneity on firm performance and systematically explores, from a governance function perspective (personnel team configuration mechanisms, incentive mechanisms, and equity allocation mechanisms), how to build a talent pipeline for innovative R&D, how to motivate employees, and how to establish a long-term oriented equity structure. Taking a systemic approach emphasizes the coupling mechanism between personnel configuration, personnel incentive, and equity allocation, highlighting their impact on the innovation governance logic of such enterprises. Thirdly, from a resource dependence perspective, the paper discusses how science-based enterprises can incorporate external governance elements into internal governance functions, fully leveraging the coupling mechanism of internal and external factors on innovation goals. To sum up, this paper enriches and expands the research framework for internal governance of science-based enterprises, providing valuable reference for the construction of theoretical models and management practices for internal governance under the Chinese context.