Presently, the practice of scientific crowdsourcing still suffers from user loss, platform operational inefficiency, and many other dilemmas, mainly because the process mechanism of realizing value co-creation through interaction between users and platforms has not yet been elaborated. To fill this gap, this study takes Kaggle as the research object and explores the realization process and internal mechanism of scientific crowdsourcing value co-creation from the perspective of knowledge flow. The results show that the operation process of Kaggle-based scientific crowdsourcing can be decomposed into five progressive evolutionary stages, including knowledge sharing, knowledge innovation, knowledge dissemination, knowledge application, and knowledge advantage formation. The knowledge flow activates a series of value co-creation activities of scientific crowdsourcing, forming a dynamic evolution and continuous optimization of the value co-creation process that includes the value proposition, value communication, value consensus, and all-win value. Institutional logic plays a key role as a catalyst in the value co-creation of scientific crowdsourcing, effectively facilitating the realization of value co-creation by controlling and guiding the flow of knowledge. The study unlocks the “gray box” from knowledge flow to value co-creation, providing new theoretical support and guidance for further enhancing the value co-creation capacity and accelerating the practice of scientific crowdsourcing.