PurposeReputation plays an increasingly decisive role in shaping the dynamics of scientific publishing. This study examines the effects of the 2020 Chinese Academy of Sciences (CAS) early-warning list of journals, which generated major shifts in Chinese scholars’ publishing behaviors and reshaped the Open Access (OA) landscape. Design/methodology/approachWe analyze 2,050,088 publications authored by 236,078 Chinese scholars across 10,006 journals between 2016 and 2024. Building an author–journal–year panel, we exploit the CAS early-warning list as an exogenous reputational shock. Difference-in-differences models are used to estimate how authors adjusted their journal choices in response to this intervention. FindingsResults show a collective and persistent withdrawal from flagged journals, consistent with a reputation trap: once stigmatized, journals experience lasting declines in submissions. The reputational damage extends to publishers, especially “grey” OA-oriented ones such as MDPI and Frontiers, whose entire portfolios lose credibility. Despite some listed titles belonging to the major international publishers, these incumbents strengthened their market position, capturing displaced submissions. Between 2020 and 2024, grey publishers lost about ten percentage points of market share, while established international houses gained accordingly. Traditional certification mechanisms, such as inclusion in Web of Science or Scopus, offered no protection against reputational loss. Research limitationsThe study focuses on Chinese scholars and the journals affected by the CAS list. Further research could assess whether similar reputation-driven dynamics emerge in other national contexts or under different institutional frameworks. Practical implicationsThe findings highlight the vulnerability of certain OA business models to reputational shocks and show how policy interventions, even when designed to improve research integrity, can inadvertently reinforce market concentration among dominant publishers. Originality/valueThis study provides the first large-scale empirical evidence of how institutional reputation mechanisms reshape the structure of scientific publishing. It contributes to understanding the unintended consequences of reputational governance on the global OA ecosystem.